Biology subjects

Mattison, C.

Publications and source records attributed to Mattison, C..

3 recordsLinked to original sources

bioRxiv2026

Multiscale harmonization and semantic integration of biomedical data enable biological insights through immersive exploration

Single-cell atlassing efforts like the Human BioMolecular Atlas Program (HuBMAP) and the Cellular Senescence Network (SenNet) are producing multiscale datasets across the healthy, adult, human body, but this data is typically explored only on 2D screens with limited 3D affordances, even though understanding a cells location within a tissue, organ, and body requires reasoning across many orders of spatial magnitude. The Human Reference Atlas (HRA) provides standard terminologies and a Common Coordinate Framework (CCF) for harmonizing such data spatially and semantically. Building on the HRA Organ Gallery in virtual reality (VR) application, we present "HRA: Powers of Ten," which integrates, harmonizes, and visualizes biological data from these efforts immersively in VR using a Multiscale Elevator System that lets users descend, like riding an elevator through an inverted skyscraper, from a whole body view of 81 reference organs to datasets across 5 organs (lymph node, brain, large intestine, small intestine, liver), 5 assay types (CODEX, Visium, v-CyCIF, Xenium, SBF-SEM), and 4 spatial scales. Contributed by Data Providers, these VR scenes enable biological insights into senescence patterns, cellular neighborhoods, 3D tissue reconstruction, and subcellular liver architecture. A standard operating procedure supports adding further datasets. Freely available on the Meta Store to over 20 million headset owners, the application, data, and code are open-source.

bioinformatics↗

bioRxiv2025

Cell type-specific associations with Alzheimer's Disease conserved across racial and ethnic groups

Genomic studies at single-cell resolution have implicated multiple cell types associated with clinical and pathological traits in Alzheimers Disease (AD), but have not examined common features across broad, multi-ethnic populations, and across multiple regions. To bridge this gap, we performed single-nucleus RNA-seq and ATAC-seq profiling of cortical and subcortical brain regions from post-mortem samples across Non-Latin White, African American, and Latin donors (the latter of any race). Using discrete and continuous dissection of molecular programs, we elucidate cell-type-specific glial and neuronal signatures associated with AD across multiple population groups. Notably, we found that multiple microglial (GPNMB+, CD74+, and CR1+ subgroups) and astrocyte (SERPINH1+ and WIF1+ subgroups) signatures are associated with worse clinical and pathological phenotypes across all three population groups. We also report continuous gene expression factors in oligodendrocytes that are not captured by discrete clusters, yet still show strong associations with disease phenotypes. Finally, we observe these discrete cellular identities and continuous gene programs separate cognitively impaired donors into 6 molecularly distinct subgroups that span racial and ethnic population groups. Overall, our study identifies key cell types and gene programs implicated in AD that are shared across population groups, and provides an initial data set that underscores how representative sampling can capture conserved signatures as well as disease heterogeneity, leading to better prioritization of key cell types for further investigation.

neuroscience↗

bioRxiv2025

Uncovering the Signatures of Cellular Senescence in the Human Dorsolateral Prefrontal Cortex

Identifying senescent cells poses challenges due to their rarity, heterogeneity, and lack of a definitive marker. We performed Visium spatial transcriptomics (ST) and single nucleus RNA sequencing (snRNA-seq) on non-pathological human tissue to build a transcriptomic atlas of aging and senescence in the dorsolateral prefrontal cortex (dlPFC). We identified markers characteristic of aging dlPFC cortical layers and cell types. We also observed an increase in astrocyte abundance and decrease in somatostatin expressing inhibitory neurons. Overall, the senescence profile in the dlPFC was highly heterogeneous and heavily influenced by cell type identity and cortical layer. Combined unbiased analysis of ST and snRNA-seq datasets revealed gene expression modules encoding for communities of microglia and endothelial cells in the white matter and regional astrocytes programs that were strongly enriched with age and for senescence-related genes. These findings will help facilitate future studies exploring the function of senescent cell subpopulations in the aging brain.

cell biology↗