Biology subjects

Spendlove, M. D.

Publications and source records attributed to Spendlove, M. D..

4 recordsLinked to original sources

bioRxiv2026

The Microglia Forebrain Assembloid Model Recapitulates Human Brain Development and Neuroimmune Biology.

Microglia are innate immune cells of the CNS whose dysfunction contributes to inflammation and metabolic changes across neurodegenerative and CNS disorders. Across all stages of life, microglia are essential for immune surveillance, neural homeostasis, and synaptic pruning; however, their role in neurodevelopment is less understood. Microglia invade the brain during early neurogenesis, prior to neuronal/glial differentiation, but their potential role at this stage remains undescribed. To model neuroimmune interactions during human cortical development, we created an "assembloid" of human ESC-derived forebrain organoids combined with developmentally matched microglia during cortex formation. Functional contributions of microglia were compared to control organoids using histology and metabolomics.

neuroscience↗

bioRxiv2026

Representation Methods of Transcriptomics with Applications in Neuroimmune Biology

Interpretable representations of gene expression are used to define cellular identities and the molecular programs active within cells, two related, but distinct phenomena. In the case of microglia, a cell type with high transcriptomic, functional, and morphological heterogeneity, the predominant representation of transcriptomic data presumes the adoption of distinct molecular identities, despite a lack of easily separable transcriptional states. Here, we explore alternative transcriptomic representations by comparing two single-cell analysis methods: differential expression analysis for identities and co-expression network analysis for molecular programs. For microglia, co-expression network analysis identifies highly significant functional ontologies not resolved by differential expression analysis. The identified co-expression modules are preserved across transcriptomic datasets and suggest reducible functional programs that activate and modulate depending on context. We conclude that co-expression analysis constitutes a best practice for single cell analysis of an individual cell type and describing microglia function as concurrent molecular programs offers a more parsimonious model of microglia function.

bioinformatics↗

bioRxiv2025

GPU-accelerated, self-optimizing processing for 3D multiplexed iterative RNA-FISH experiments

Imaging-based spatial transcriptomic approaches rely on iterative labeling and imaging of carefully prepared samples, followed by solving a computational inverse problem to determine the location and identity of the targeted RNA. Because these approaches require high-resolution optics, the Nyquist-Shannon determined voxel size is small relative to typical tissue sample footprints. A common solution to speed up both experiments and computation is to increase the distance in between focal planes, trading off local information content to sample a larger imaging area in a reasonable time. In this work we introduce a GPU-accelerated computational framework, merfish3d-analysis, designed to speed up the computational processing of barcoded, in situ imaging-based spatial transcriptomics. Using this framework, we quantify the information lost due to axial sampling changes in simulated imaging-based spatial transcriptomic experiments, robustly reprocess publicly available multiplexed error-robust fluorescence in situ hybridization (MERFISH) datasets, and analyze new MERFISH experiments performed on a post-mortem human olfactory bulb sample. To improve the quality of experimental data in the post-mortem human sample, we designed a multi-step autofluorescence quenching protocol specific for in situ imaging-based spatial transcriptomic strategies. Taken together, we hope that the sample preparation protocols and single workstation, GPU-accelerated processing will further democratize imaging-based spatial transcriptomic experiments.

bioinformatics↗

bioRxiv2024

CRIPTO promotes extracellular vesicle uptake and activation of fibroblast exposed to triple negative breast cancer cells

Expression of CRIPTO, a factor involved in embryonic stem cells, fetal development, and wound healing, is tied to poor prognosis in multiple cancers. Prior studies in triple negative breast cancer (TNBC) models showed CRIPTO blockade inhibits tumor growth and dissemination. Here, we uncover a previously unidentified role for CRIPTO in orchestrating tumor-derived extracellular vesicle (TEV) uptake and fibroblast activation through discrete mechanisms. We found a novel mechanism by which CRIPTO drives aggressive TNBC phenotypes, involving CRIPTO-laden TEVs that program stromal fibroblasts, toward cancer associated fibroblast cell states, which in turn prompt tumor cell invasion. CRIPTO-bearing TEVs exhibited markedly elevated uptake in target fibroblasts and activated SMAD2/3 through NODAL-independent and - dependent mechanisms, respectively. Engineered expression of CRIPTO on EVs enhanced the delivery of bioactive molecules. In vivo, CRIPTO levels dictated TEV uptake in mouse lungs, a site of EV-regulated premetastatic niches important for breast cancer dissemination. These discoveries reveal a novel role for CRIPTO in coordinating heterotypic cellular crosstalk which offers novel insights into breast cancer progression, delivery of therapeutic molecules, and new, potentially targetable mechanisms of heterotypic cellular communication between tumor cells and the TME.

cancer biology↗