Biology subjects

Summers, M.

Publications and source records attributed to Summers, M..

3 recordsLinked to original sources

bioRxiv2026

3D-MAESTRO: A scalable, modular, portable pipeline for automated processing of large-scale volumetric brain microscopy data

Light microscopy is routinely used to explore the cellular and molecular structure of tissues, but the scale and complexity of data remains a bottleneck for discovery. We introduce 3D-MAESTRO (3D-Microscopy Automation and Execution with Scalable Tools, Rendering, and Orchestration): an automated image processing workflow for large-scale microscopy data, built for scalable execution across cloud and local computing environments. 3D-MAESTRO orchestrates denoising, stitching of image tiles, atlas registration, and segmentation. Its modular architecture permits the integration and benchmarking of new packages, ensuring that performance evolves as more efficient or accurate algorithms emerge. We introduce a new 3D image template for automated registration of mouse brains cleared with aqueous reagents and an efficient method for detection of fluorescent cells. We apply 3D-MAESTRO to lightsheet images of whole mouse brains in the context of diverse anatomical and functional experiments, illustrating high-throughput and reproducible mapping of microscopic structures across the brain.

neuroscience↗

bioRxiv2026

Stepwise Evolution and Epistatic Interaction of Driver Mutations from Endometrial Hyperplasia to Carcinoma

To characterize early oncogenesis, pathologically identified pre-cancerous tissue can be analyzed for the presence of cancer drivers. Here, we argue that in such studies, analyses of the driver status of variants, of the association between step-specific prevalence and progression through tumorigenesis, and of driver co-occurrence and mutual exclusivity should be accompanied by estimates of inherent mutation rate of variants and presented within an evolutionary framework of selective epistasis. To illustrate this point, we examine the transition of endometrial tissue from atypical hyperplasia to carcinoma. We apply a step-specific analysis, demonstrating that the strength of selection on somatic driver mutations promoting cell division and survival differs between hyperplasia to carcinoma. We demonstrate that mutations of PTEN, which are highly prevalent in carcinomas and have been argued to exert substantial driver effects, exhibit an even larger effect of increasing cellular division and survival within developing hyperplasias. A determination of cooccurrence or mutual exclusivity may be a product of genes sharing or differing in underlying sources of mutation, as opposed to a product of biological interaction and selection. By accounting for tumor-specific mutational processes that influence co-occurrence, we calculate epistatic selective intensities between pairs of drivers. Mutations of KRAS and FGFR2 are often mutually exclusive and were indeed found to exhibit significant antagonistic selective epistasis. However, mutations of PIK3CA and PIK3R1, which also have been identified as showing mutual exclusivity, do not demonstrate significant antagonistic selective epistasis. Thus, evidence of mutually exclusivity is insufficient to determine epistasis. Accordingly, the application of quantitative approaches that distinctly analyze mutation and selection on cancer variants has the potential to substantially illuminate the trajectory of tumorigenesis and cancer progression.

Cancer Biology↗

bioRxiv2026

Endothelium-Dependent Vasodilation is Impaired in Chronic Spinal Cord Injury and is Associated with Oxidative Stress

BackgroundIndividuals with spinal cord injury (SCI) experience accelerated atherosclerotic cardiovascular disease that is not fully explained by traditional risk factors. Endothelial dysfunction is a key mechanism in atherosclerosis. We tested the hypothesis that endothelium-dependent vasodilation is impaired in adults with SCI and is due, at least in part, to oxidative stress. MethodsTwenty-four adults (age:19-58 yr) free of overt cardiometabolic disease were studied: 12 non-injured adults (9 M/3 F) and 12 adults with chronic SCI (8 M/4 F; time since injury 1.5 - 25 years). Forearm blood flow was determined (FBF; via strain-gauge plethysmography) in response to intra-arterial infusion of acetylcholine and isoproterenol in the absence and presence of the antioxidant vitamin C as well as the FBF response to sodium nitroprusside. ResultsAdults with SCI demonstrated significantly lower vasodilator response to acetylcholine (from 4.1{+/-}0.6 to 10.7{+/-}2.6 mL/100 mL tissue/min vs 4.1{+/-}1.1 to 15.7{+/-}3.4 mL/100 mL tissue/min) and isoproterenol (4.0{+/-}0.6 to 11.2{+/-}2.2 mL/100 mL tissue/min vs 4.3{+/-}1.0 to 15.0{+/-}2.6 mL/100 mL tissue/min) compared with non-injured adults. FBF response to sodium nitroprusside was not significantly different between the groups. Co-infusion of vitamin C significantly increased the vasodilator response to acetylcholine (~45%) and isoproterenol (~25%) in the adults with SCI to levels comparable with non-injured adults. ConclusionsChronic SCI is associated with endothelial-dependent vasodilator dysfunction. Impaired vasodilation across two distinct endothelial agonists suggests that chronic SCI is associated with endothelial dysfunction not confined to a specific receptor or intracellular signaling pathway. Moreover, oxidative stress is a contributing factor underlying SCI-related endothelial vasodilator dysfunction. NCT06443151 CLINICAL PERSPECTIVEO_LIThe novel finding of this study is that individuals with SCI demonstrate impaired endothelial vasodilator function in absence of traditional cardiovascular risk factors. C_LIO_LIOxidative stress is a contributing factor to SCI-related endothelial vasodilator dysfunction. C_LIO_LIFuture studies are needed to determine the efficacy of therapeutic interventions, either lifestyle or pharmacologic, in improving endothelial function in order to mitigate the elevated ASCVD risk after SCI. C_LI

physiology↗