Biology subjects

Cavanaugh, C.

Publications and source records attributed to Cavanaugh, C..

5 recordsLinked to original sources

bioRxiv2026

Connectome quality converges predictably to reveal optimal stopping points during proofreading

Volumetric electron microscopy (EM) has become a critical approach to generating high-resolution reconstructions of brain tissue. As the size of EM volumes increase, use of automated image segmentation within the reconstruction pipeline has become essential, although it generates errors that need correction. The proofreading and correcting of these errors has since become the dominant cost driver in the pipeline, but precisely estimating the sufficient number of proofreading edits to enable meaningful scientific analyses of the reconstructed neuronal networks remains a challenge. We present a fast, computationally inexpensive way to estimate the progress of a connectomic proofreading effort without requiring a priori knowledge of ground truth. We show that simple global graph invariants converge predictably to asymptotic limits with increasing numbers of proofreading edits, informing a quantitative "pencils down" criterion for proofreading completeness. We illustrate our method on two datasets in different stages of proofreading progress, a zebrafish spinal cord and the hemibrain Drosophila melanogaster dataset. Our method reduces the uncertainty associated with the planning and prioritization of proofreading activities and enables data owners to accurately predict and budget the amount of proofreading necessary for their scientific questions.

neuroscience↗

bioRxiv2025

Genetic dissection of microglia cannibalism reveals an IL10 signaling axis controls microglia lifespan

The development of complex organs, like the brain, demands a robust system for tissue remodeling and cellular debris clearance. In the brain, this function is performed by microglia, which must clear diverse debris substrates, including that caused by cell death. Although the subsequent fate of these phagocytic microglia is a critical regulatory point that impacts whether the brain resolves a debris environment, the genetic mechanisms that control microglia fate after debris clearance remain mostly unknown. To address this, we conducted a large-scale CRISPR screen in zebrafish using a custom-built robotic confocal microscope. We selected candidate genes from a single-cell RNA sequencing dataset of embryonic mouse microglia. This screen identified several modulators of microglial lifespan and cannibalism that are enriched in mouse and zebrafish microglia, including interleukin-10 receptor beta (il10rb), a receptor subunit for the cytokine IL10. Perturbation of il10, il10rb, and downstream signaling molecules JAK/STAT in zebrafish reduced microglial death. Expression analysis in mouse and zebrafish confirmed that microglia express both il10 and il10rb. Given the established role of IL10 in lysosomal remodeling, we hypothesized that it regulates microglial survival through lysosomal acidification. While il10rb perturbation did not alter lysosome number or size, it caused a significant reduction in LysoTracker-positive lysosomes, indicating decreased lysosomal acidification. Inhibiting v-ATPase also reduced microglial death, reinforcing the link between lysosomal pH and cell fate. Our findings reveal a cytokine-regulated mechanism where lysosomal dynamics determine the survival of phagocytic microglia. We propose that a necroptosis-cannibalism process functions as a quality control mechanism for microglial turnover, which is critical for refining neuroimmune cell function in the brain.

neuroscience↗

bioRxiv2025

Transcriptomic Response to Neuromuscular Electrical Stimulation in Muscle, Brain and Plasma EVs in WT and Klotho-deficient Mice

Neuromuscular electrical stimulation (NMES) was shown to improve motor activities and daily living. Prior studies indicated extracellular vesicles (EVs) play a role in cellular communication. Here, we evaluated transcriptomic profiles of tibialis anterior muscle, brain, and plasma-derived EVs following NMES of WT and Klotho heterozygous (KlHET). Muscle RNA-seq data demonstrated that in both genotypes the most upregulated functional categories were related to glucose metabolism and response to insulin with pathways uniquely affected in each genotype. There was a similarity of non-coding RNA transcriptome of plasma EVs with functional patterns suggesting response to oxygen and insulin, and long-term synaptic potentiation. Brain transcriptome showed little functional overlap between WT and KlHET mice. In WT, brain upregulation of genes were related to blood flow and cell adhesion processes while KlHET shows upregulation of immune function. Results indicate that similar metabolic function is impacted in the location of stimulation, but the distal impact of stimulation on the brain is associated with Klotho deficiency.

genomics↗

bioRxiv2024

Role of CCK1 receptor in metabolic benefits of intestinal enteropeptidase inhibition in mice

Enteropeptidase (EP; enterokinase) is a serine protease that regulates intestinal protein digestion by converting trypsinogen into active trypsin, and thus initiates activation of the pancreatic zymogen cascade. Chronic inhibition of EP and trypsin (EP/T) with camostat (Foipan, FOY-305) or its active metabolite (FOY-251) causes weight loss in obese mice by reducing intestinal protein absorption and suppression of food intake, however, the mechanisms leading to appetite suppression are not well understood. We tested the hypothesis that cholecystokinin (CCK) signaling mediates the anorectic effects of EP/T inhibition using a CCK1R inhibitor (loxiglumide) or CCK1R knockout (KO) mice. Acute treatment with loxiglumide was able to partially reverse FOY-251-induced gallbladder contraction and delayed gastric emptying in mice. Chronic co-administration of loxiglumide reversed FOY-251 mediated effects on food intake and metabolism in diet-induced obese (DIO) mice. Chronic dosing of FOY-251 caused similar reductions in food intake but greater weight loss in CCK1R KO mice compared to wildtype (WT) mice, primarily due to fat mass loss. Pair fed (PF) groups revealed food intake-dependent and -independent mechanisms of weight loss by FOY-251. Notably, FOY-251 treatment induced sustained weight loss, whereas body weight loss rebounded in PF animals. In CCKR1 KO mice, FOY-251 caused greater weight loss, and increased protein calorie loss relative to that in WT mice, while having no effect on glycemic control or FGF21. Hence, CCK1R-dependent and - independent mechanisms modulate the metabolic effects of EP/T inhibition and may play a role in maintaining weight loss by this mechanism.

pharmacology and toxicology↗

bioRxiv2017

Using DNase Hi-C techniques to map global and local three-dimensional genome architecture at high resolution

The folding and three-dimensional (3D) organization of chromatin in the nucleus critically impacts genome function. The past decade has witnessed rapid advances in genomic tools for delineating 3D genome architecture. Among them, chromosome conformation capture (3C)-based methods such as Hi-C are the most widely used techniques for mapping chromatin interactions. However, traditional Hi-C protocols rely on restriction enzymes (REs) to fragment chromatin and are therefore limited in resolution. We recently developed DNase Hi-C for mapping 3D genome organization, which uses DNase I for chromatin fragmentation. DNase Hi-C overcomes RE-related limitations associated with traditional Hi-C methods, leading to improved methodological resolution. Furthermore, combining this method with DNA capture technology provides a high-throughput approach (targeted DNase Hi-C) that allows for mapping fine-scale chromatin architecture at exceptionally high resolution. Hence, targeted DNase Hi-C will be valuable for delineating the physical landscapes of cis-regulatory networks that control gene expression and for characterizing phenotype-associated chromatin 3D signatures. Here, we provide a detailed description of method design and step-by-step working protocols for these two methods.\n\nHighlightsO_LIDNase Hi-C, a method for comprehensive mapping of chromatin contacts on a whole-genome scale, is based on random chromatin fragmentation by DNase I digestion instead of sequence-specific restriction enzyme (RE) digestion.\nC_LIO_LITargeted DNase Hi-C, which combines DNase Hi-C with DNA capture technology, is a high-throughput method for mapping fine-scale chromatin architecture of genomic loci of interest at a resolution comparable to that of genomic annotations of functional elements.\nC_LIO_LIDNase Hi-C and targeted DNase Hi-C provide the first high-throughput way to overcome the RE-digestion-associated resolution limit of 3C-based methods.\nC_LIO_LIStep-by-step whole-genome and targeted DNase Hi-C protocols for mapping global and local 3D genome architecture, respectively, are described.\nC_LI

genomics↗