Biology subjects

Boyer, L. A.

Publications and source records attributed to Boyer, L. A..

5 recordsLinked to original sources

bioRxiv2026

HiExM Enables Scalable Mapping of Organelle Morphology and Spatial Heterogeneity

Quantitative image analysis of subcellular organization requires sufficient spatial resolution to resolve individual organelles and sample size to capture heterogeneity both within cells and between cells. Existing imaging approaches often force a tradeoff between spatial resolution and throughput, limiting the ability to measure organelle-level phenotypes across cell populations. Here, we establish high-throughputs expansion microscopy (HiExM) as a scalable pipeline for single-organelle analysis. As a benchmark, we focus on mapping late endosomes and lysosomes (LELs), a heterogeneous organelle class whose small size, dense intracellular distribution, and functional diversity make it difficult to quantify accurately using conventional light microscopy. HiExM increases effective spatial resolution while preserving compatibility with large-scale image acquisition, enabling robust segmentation and quantitative profiling of individual LELs across large cell populations. Using this pipeline, we identified differences in intracellular trafficking behavior among anti-transferrin receptor antibodies that could not be captured by conventional colocalization analysis alone. We further integrate spatial and morphological features with learned image-based representations that can define relationships between LEL morphology and subcellular position as well as how these relationships respond to perturbations. Together, our work establishes HiExM as a generalizable platform for scalable single-organelle profiling, enabling an analytical framework for quantifying discrete organelles across cells and conditions.

cell biology↗

bioRxiv2025

CFDP1 is required for histone variant H2A.Z deposition by the human SRCAP chromatin remodeling complex

Craniofacial Developmental Protein 1 (CFDP1) is a member of the evolutionarily conserved family of Bucentaur (BCNT) proteins and was originally classified as a protein required for cell survival and differentiation during tooth development. Yeast Swc5, a BCNT family member, is an essential subunit of the yeast SWR1C chromatin remodeling complex that catalyzes the deposition of histone variant H2A.Z. Direct connections between CFDP1, H2A.Z deposition, and the mammalian SWR1 homolog, Snf2-Related CREBBP Activator Protein (SRCAP), have not been identified. Here, we perform detailed biochemical reconstitution and characterization of the human SRCAP complex (SRCAP-C). We find that CFDP1 weakly interacts with SRCAP-C in a salt concentration-dependent manner. SRCAP-C purified under a high-salt condition does not co-purify with CFDP1 and is inactive in H2A.Z dimer exchange reaction, but the addition of exogeneous CFDP1 restores the H2A.Z deposition activity of SRCAP-C, demonstrating that CFDP1 is required for H2A.Z dimer exchange by SRCAP-C. We show that CFDP1 stimulates the basal ATPase activity of reconstituted SRCAP-C, suggesting a requirement for CFDP1 in regulating intrinsic catalytic ATPase activity. Consistent with this idea, CFDP1 deficiency in human induced pluripotent stem cells (hiPSCs) leads to a genome-wide reduction of H2A.Z, H3K27me3, and H3K4me3 deposition, accompanied by the upregulation of developmental genes normally marked by these modifications. Taken together, our results provide mechanistic insights into how CFDP1 regulates histone variant H2A.Z deposition by SRCAP-C. Given mutations in the SRCAP gene cause Floating-Harbor syndrome (FHS), a rare, dominant developmental disorder, our study provides an additional link between craniofacial defects and SRCAP-mediated H2A.Z deposition.

molecular biology↗

bioRxiv2025

Self-amplifying RNA enables rapid, durable, integration-free programming of hiPSCs

Genetic modification of human induced pluripotent stem cells (hiPSCs) is a powerful approach to measure and manipulate the cellular processes underlying differentiation and disease. Conventional genetic engineering of hiPSC lines requires a laborious process involving transfection, selection and expansion that can result in karyotypic abnormalities or transgene silencing during differentiation, limiting their applications. Self-amplifying RNA (saRNA) delivery is a potential alternative integration-free method for durable expression of transgenes. Here, we used saRNA to deliver transcription factors and functional reporters in hiPSCs and demonstrate that expression can persist for weeks. Specifically, saRNA delivery enables highly efficient forward programming to Ngn2-induced neurons and enables measurement of functional reporters over time. We show that a single transfection of saRNA encoded jRCaMP1b reporter in hiPSCs generates sustained expression throughout differentiation to 3D cardiac spheroids. The persistence of the reporter allows measurement of calcium dynamics at a single-cell and population level over weeks, allowing tracking of cardiomyocyte maturation and drug responses. Together, our systematic analysis shows that saRNA provides sustained transgene expression in hiPSCs, supporting integration- free cell-fate programming and measurement of functional reporters in clinically relevant model systems. HighlightsO_LIA single saRNA transfection generates durable transgene expression C_LIO_LIsaRNA transfection of Ngn2 in hiPSCs results in robust neuronal differentiation C_LIO_LIsaRNA-delivery of functional reporters enables single-cell analysis of primary and hiPSC-derived cells C_LIO_LIsaRNA-based sensor allows monitoring of maturation and drug responses in 3D cardiac spheroids C_LI

bioengineering↗

bioRxiv2025

Assessment of dispersion metrics for estimating single-cell transcriptional variability

Single-cell RNA sequencing data enables analysis of transcript levels of single cells across different cell types and conditions. Recent work has highlighted the value of measuring gene-specific transcriptional variability, or noise, within a genetically identical population of cells in addition to mean expression given that these differences contribute to biological processes including development and disease. However, measuring transcriptional noise remains a challenge. Here, we systematically compared statistical methods by simulating single-cell data by varying both dispersion and count size to assess the relative responsiveness to noise of several commonly used statistical metrics: the Gini index, variance-to-mean ratio, variance, and Shannon entropy. We found that the variance-to-mean ratio scales approximately linearly with increasing dispersion and is scale-invariant. In contrast, the Gini index displayed paradoxical behavior, and Shannon entropy was not scale-invariant. Thus, we next applied the variance-to-mean ratio to measure transcriptional variability in a publicly available single-cell dataset of embryonic hearts from a mouse model of maternal hyperglycemia. Our data show that many genes display transcriptional variability within the same cell type, and that this variation does not correlate with gene characteristics such as transcript level, promoter GC content, or evolutionary gene age. Notably, many of the genes and pathways with highest transcriptional variability were not identified as differentially expressed, and have in fact been implicated in maternal hyperglycemia in other studies, suggesting that transcriptional variability can provide additional biologically relevant information beyond what is observed from studying mean expression alone.

genomics↗

bioRxiv2023

HiExM: high-throughput expansion microscopy enables scalable super-resolution imaging

Expansion microscopy (ExM) enables nanoscale imaging using a standard confocal microscope through the physical, isotropic expansion of fixed immunolabeled specimens. ExM is widely employed to image proteins, nucleic acids, and lipid membranes in single cells; however, current methods limit the number of samples that can be processed simultaneously. We developed High-throughput Expansion Microscopy (HiExM), a robust platform that enables expansion microscopy of cells cultured in a standard 96-well plate. Our method enables [~]4.2x expansion of cells within individual wells, across multiple wells, and between plates. We also demonstrate that HiExM can be combined with high-throughput confocal imaging platforms to greatly improve the ease and scalability of image acquisition. As an example, we analyzed the effects of doxorubicin, a known cardiotoxic agent, on human cardiomyocytes (CMs) as measured by Hoechst signal across the nucleus. We show a dose dependent effect on nuclear DNA that is not observed in unexpanded CMs, suggesting that HiExM improves the detection of cellular phenotypes in response to drug treatment. Our method broadens the application of ExM as a tool for scalable super-resolution imaging in biological research applications. Significance StatementExpansion microscopy (ExM) is an accessible and widely used technique for super-resolution imaging of fixed biological specimens. For many ExM users, slide-based sample preparation and manual imaging limit the number of experimental conditions and samples that can be processed in parallel. Here, we develop a simple and inexpensive device that enables ExM within the wells of a standard 96-well cell culture plate. We show that samples prepared with our workflow can be imaged with a high-throughput autonomous confocal microscope, allowing for scalable super-resolution image acquisition, greatly increasing data output. Our device retains the accessibility of ExM while extending its application to research questions that require the analysis of many conditions, treatments, and time points.

bioengineering↗