Biology subjects

Bartosik, W.

Publications and source records attributed to Bartosik, W..

3 recordsLinked to original sources

bioRxiv2024

Single-cell analysis of the epigenome and 3D chromatin architecture in the human retina

Most genetic risk variants linked to ocular diseases are non-protein coding and presumably contribute to disease through dysregulation of gene expression, however, deeper understanding of their mechanisms of action has been impeded by an incomplete annotation of the transcriptional regulatory elements across different retinal cell types. To address this knowledge gap, we carried out single-cell multiomics assays to investigate gene expression, chromatin accessibility, DNA methylome and 3D chromatin architecture in human retina, macula, and retinal pigment epithelium (RPE)/choroid. We identified 420,824 unique candidate regulatory elements and characterized their chromatin states in 23 sub-classes of retinal cells. Comparative analysis of chromatin landscapes between human and mouse retina cells further revealed both evolutionarily conserved and divergent retinal gene-regulatory programs. Leveraging the rapid advancements in deep-learning techniques, we developed sequence-based predictors to interpret non-coding risk variants of retina diseases. Our study establishes retina-wide, single-cell transcriptome, epigenome, and 3D genome atlases, and provides a resource for studying the gene regulatory programs of the human retina and relevant diseases.

genomics↗

bioRxiv2024

Epigenetic and 3D genome reprogramming during the aging of human hippocampus

Age-related cognitive decline is associated with altered physiology of the hippocampus. While changes in gene expression have been observed in aging brain, the regulatory mechanisms underlying these changes remain underexplored. We generated single-nucleus gene expression, chromatin accessibility, DNA methylation, and 3D genome data from 40 human hippocampal tissues spanning adult lifespan. We observed a striking loss of astrocytes, OPC, and endothelial cells during aging, including astrocytes that play a role in regulating synapses. Microglia undergo a dramatic switch from a homeostatic state to a primed inflammatory state through DNA methylome and 3D genome reprogramming. Aged cells experience erosion of their 3D genome architecture. Our study identifies age-associated changes in cell types/states and gene regulatory features that provide insight into cognitive decline during human aging.

genomics↗

bioRxiv2019

The cytoprotective role of antioxidants in mammalian cells under rapidly varying temperature, pressure and UV conditions during stratospheric balloon campaign

1.Currently ongoing age of the dynamic development of the space industry brings the mankind closer to the routine manned space flights and space tourism. That progress leads to a demand for intensive astrobiological research aimed at improving strategies of the pharmacological protection of the human cells against extreme conditions. Although routine research in space remain out of our reach, it is worth noticing that unique severe environment of the Earths stratosphere have been found to mimic subcosmic conditions, giving rise to the opportunity for use of stratospheric surface as a research model for the astrobiological studies. Our study included launching balloon into the stratosphere containing the human normal and cancer cells treated with various compounds to examine whether these medicines are capable to protect the cells against the stress caused by rapidly varying temperature, pressure and radiation, especially UV. Due to oxidative stress caused by irradiation and temperature shock, we used natural compounds which display antioxidant properties, namely catechin isolated from green tea, honokiol derived from magnolia, curcumin from turmeric and cinnamon extract. "After-flight" laboratory tests displayed the most active antioxidants as potential agents which can minimize harmful impact of extreme conditions to the human cells.

cell biology↗