Biology subjects

Bowman, C.

Publications and source records attributed to Bowman, C..

15 recordsLinked to original sources

bioRxiv2026

Novel 3D Mature Osteocyte Perfusion Platform Reveals Subtype-Dependent and Radiation-Sensitive Disruption of Mechanotransduction by Breast Cancer Secretomes

Osteocytes (OCys) coordinate bone remodeling by transducing mechanical signals into anabolic cues, primarily through suppressing sclerostin and RANKL. In breast cancer (BCa) bone metastasis, mechanical loading fails to restore lost bone, pointing to tumor-induced OCy mechanosensory dysfunction. Here, we investigate how BCa molecular subtype heterogeneity and frontline therapies like radiation influence OCy mechanobiology. We leveraged a 3D mineralized scaffold paired with a forced perfusion bioreactor to establish a physiologically relevant model of mature, dendrite-bearing OCys. After optimizing perfusion parameters, 3D mature OCys were exposed to conditioned media (CM) from estrogen receptor-positive (ER+; ZR-75-1) or triple-negative (TN; MDA-MB-231) BCa cells generated 24 h post-irradiation (0 vs. 2 Gy). Downstream OCy gene expression (Sost, Tnfsf11, Tnfrsf11b) and tumor CM proteomic profiles (84 oncology targets) were evaluated. Differentiated 3D MPC-2s exhibited interconnected dendritic networks, classical responsiveness to parathyroid hormone, and robust flow-induced Sost suppression. Non-irradiated ER+ BCa CM preserved canonical OCy mechanoresponsiveness (Sost downregulation post-flow), but this response was eliminated when ER+ cells received 2 Gy radiation. Conversely, TN CM blunted flow-induced Sost suppression regardless of irradiation status. Proteomic profiling revealed that BCa subtype was the primary driver of secretome composition, whereas 2 Gy radiation induced distinct directional secretome shifts between subtypes. These findings demonstrate that BCa-induced impairment of OCy mechanosensing is subtype-dependent and that low-dose radiation further exacerbates secretome-mediated mechanosensory loss in ER+ disease, highlighting key tumor-derived targets for restoring skeletal health.

bioengineering↗

bioRxiv2026

An age-preserving neuronal iSpheroid platform for modeling human aging and Alzheimer disease

Aging is the strongest risk factor for Alzheimer disease (AD), yet existing human neuronal models either erase age-associated features during reprogramming or fail to recapitulate three-dimensional organization of human neuronal tissue. Here, we establish directly induced neuronal spheroids (iSpheroids), a scalable three-dimensional platform generated by direct conversion of primary fibroblasts without pluripotency. iSpheroids generate long-lived, electrophysiologically active neurons from young, unimpaired aged, and sporadic AD donors while preserving donor-specific epigenetic age. Single-nucleus RNA sequencing revealed approximately 96% of cells acquired a neuronal identity and were distributed across multiple neuronal states, including a diversity of neurons. The platform supports incorporation of astrocytes and microglia and generation from non-human primate fibroblasts. AD iSpheroids spontaneously recapitulated neuronal degeneration, amyloid-beta; accumulation, progressive Tau pathology, and metabolic dysfunction. Integrated proteomic, metabolomic, and lipidomic profiling distinguished physiological aging from AD and revealed disease-associated metabolic remodeling. Oxaliplatin shifted AD iSpheroids toward oxidative metabolism, whereas a multi-compound screen identified trametinib as a modulator of inflammatory and age-associated programs.

neuroscience↗

bioRxiv2026

A Multispecies, Modality-Agnostic Scalable In Vivo Mosaic Screening Platform for Therapeutic Target Discovery

Validating therapeutic targets for complex diseases requires investigating gene functions within native tissue architectures rather than reductionist in vitro models. Here we present a modality-agnostic AAV-based in vivo high-throughput screening platform capable of delivering knockouts, gain-of-function, and synthetic miRNA knockdowns directly to cells within the diseased environment. This system scales to hundreds of perturbations and is adaptable to diverse species and organ systems. To translate high-dimensional screen data into therapeutic assessment, we established a curated analysis framework that scores single-cell transcriptomes against human disease-specific molecular signatures. This method enables quantitative ranking of targets across distinct biological domains ranging from structural fibrosis to inflammatory signaling, to narrow in on the therapeutic potential of each intervention. We applied this strategy to screen loss- and gain-of-function libraries in a murine pulmonary fibrosis model and within the spontaneously osteoarthritic joints of aged horses, identifying metabolic, antifibrotic, and immunomodulatory targets. Importantly, our analysis framework successfully predicted functional outcomes in orthogonal human ex vivo tissue models, including soluble collagen reduction in lung slices and glycosaminoglycan restoration in cartilage, thus establishing a powerful paradigm for prioritizing therapeutic targets by uniting human disease signatures with highly multiplexed in vivo functional genomics.

systems biology↗

bioRxiv2025

Ventromedial prefrontal cortex supports prototype representations in healthy older adults

The ability to learn broad concepts from individual instances is relevant throughout our lifespans as new concepts enter the world, and we seek to acquire new skills and hobbies that can enrich our lives. While older age has been associated with declines in the ability to remember individual instances, less is known about how these declines impact concept learning and generalization or the neural systems that older adults recruit to support abstraction. In the present study, we used prototype-based category learning as a domain to test age differences in concept learning. Young and older adults completed a category-learning task while undergoing fMRI. We fit formal prototype and exemplar models to behavioral and brain data to index concept learning based on abstraction versus memory for individual category members. We found that the fit of both models to behavior was poorer in older adults, but older adults were more likely than young adults to be best fit by the prototype model and less likely to be best fit by the exemplar model. While only young adults showed significant prototype-tracking in the hippocampus, both young and older adults recruited the ventromedial prefrontal cortex (VMPFC) to support prototype-based generalization. Although evidence for age differences in prototype representations emerged in a whole-brain analysis, evidence for age differences were weak in the VMPFC and hippocampus. Thus, engagement of the VMPFC prototype-learning system may help maintain concept generalization in older adults.

neuroscience↗

bioRxiv2024

Adult lifespan effects on functional specialization along the hippocampal long axis

There has been increasing attention to differences in function along the hippocampal long axis, with the posterior hippocampus proposed to be well suited to representing fine-grained details and the anterior hippocampus having coarser representations. Whether long axis functional specialization persists into older age is not well understood, despite known age-related declines in the level of detail in memories. In this study, we used a large database of resting state fMRI data (n =322 humans of both sexes included) from across the adult lifespan (ages 18-88) to determine the degree of functional differentiation across the hippocampal posterior-anterior axis. Our first approach was to measure the similarity among signals within hippocampal subregions. We found that signals within the most posterior hippocampal subregion became more similar to one another in older age, but this effect did not relate to memory performance. As a second approach, we measured functional connectivity between hippocampal subregions and the rest of the brain. The functional connectivity profiles of the posterior and anterior hippocampal subregions became more distinct from one another with increasing age, driven by relative stability in anterior hippocampal functional connectivity but more significant age-related differences in posterior subregions of the hippocampus. Stronger connectivity between the anterior hippocampus and several cortical regions was associated with better memory performance in older adults, suggesting that maintenance of anterior hippocampal connectivity may help preserve episodic memory among high performing older adults.

neuroscience↗

bioRxiv2024

SGLT2 inhibitors activate pantothenate kinase in the human heart

Inhibitors of sodium glucose cotransporter-2 (SGLT2i) demonstrate strong symptomatic and mortality benefits in the treatment of heart failure but appear to do so independently of SGLT2. The relevant pharmacologic target of SGLT2i remains unclear. We show here that SGLT2i directly activate pantothenate kinase 1 (PANK1), the rate-limiting enzyme that initiates the conversion of pantothenate (vitamin B5) to coenzyme-A (CoA), an obligate co-factor for all major pathways of fuel use in the heart. Using stable-isotope infusion studies, we show that SGLT2i promote pantothenate consumption, activate CoA synthesis, rescue decreased levels of CoA in human failing hearts, and broadly stimulate fuel use in ex vivo perfused human cardiac blocks from patients with heart failure. Furthermore, we show that SGLT2i bind to PANK1 directly at physiological concentrations and promote PANK1 enzymatic activity in assays with purified components. Novel in silico dynamic modeling identified the site of SGLT2i binding on PANK1 and indicated a mechanism of activation involving prevention of allosteric inhibition of PANK1 by acyl-CoA species. Finally, we show that inhibition of PANK1 prevents SGLT2i-mediated increased contractility of isolated adult human cardiomyocytes. In summary, we demonstrate robust and specific off-target activation of PANK1 by SGLT2i, promoting CoA synthesis and efficient fuel use in human hearts, providing a likely explanation for the remarkable clinical benefits of SGLT2i.

biochemistry↗

bioRxiv2024

Microbial Hauberks: Composition and Function of Surface Layer Proteins in Gammaproteobacterial Methanotrophs

Many species of proteobacterial methane-consuming bacteria (methanotrophs) form a hauberk-like envelope represented by a surface (S-) layer protein matrix. While several proteins were predicted to be associated with the cell surface, the composition and function of the hauberk matrix remained elusive. Here we report the identification of the genes encoding the hauberk-forming protein in two gamma-proteobacterial (Type I) methanotrophs, Methylotuvimicrobium buryatense 5GB1 (EQU24_15540) and Methylotuvimicrobium alcaliphilum 20ZR (MEALZ_0971 and MEALZ_0972). The proteins share 40% AA identity with each other and are distantly related to the RsaA proteins from Caulobacter crescentus (20% AA identity). Deletion of these genes resulted in loss of the characteristic hauberk pattern on the cell surface. A set of transcriptional fusions between the MEALZ_0971 and a superfolder green fluorescent protein (sfGFP) further confirmed its surface localization. The functional roles of the hauberk and cell-surface associated proteins, including MEALZ_0971, MEALZ_0972, EQU24_15540, and a copper-induced CorA protein, were further investigated via gene expression studies and phenotypic tests. The hauberk core protein shows constitutive expression across 18 growth conditions. The M. alcaliphilum 20ZR{Delta}0971 showed reduced growth at high salinity, high methanol and metal-limited conditions, suggesting a role in cell-envelope stability and metal scavenging. Overall, understanding the genetics, composition and cellular functions of the S-layers contributes to our knowledge of methanotroph adaptation to environmental perturbations and opens a promising prospect for (nano)biotechnology applications.

microbiology↗

bioRxiv2023

Vaccine-mediated protection against merbecovirus and sarbecovirus challenge in mice

The emergence of three distinct highly pathogenic human coronaviruses - SARS-CoV in 2003, MERS-CoV in 2012, and SARS-CoV-2 in 2019 - underlines the need to develop broadly active vaccines against the Merbecovirus and Sarbecovirus betacoronavirus subgenera. While SARS-CoV-2 vaccines are highly protective against severe COVID-19 disease, they do not protect against other sarbecoviruses or merbecoviruses. Here, we vaccinate mice with a trivalent sortase-conjugate nanoparticle (scNP) vaccine containing the SARS-CoV-2, RsSHC014, and MERS-CoV receptor binding domains (RBDs), which elicited live-virus neutralizing antibody responses and broad protection. Specifically, a monovalent SARS-CoV-2 RBD scNP vaccine only protected against sarbecovirus challenge, whereas the trivalent RBD scNP vaccine protected against both merbecovirus and sarbecovirus challenge in highly pathogenic and lethal mouse models. Moreover, the trivalent RBD scNP elicited serum neutralizing antibodies against SARS-CoV, MERS-CoV and SARS-CoV-2 BA.1 live viruses. Our findings show that a trivalent RBD nanoparticle vaccine displaying merbecovirus and sarbecovirus immunogens elicits immunity that broadly protects mice against disease. This study demonstrates proof-of-concept for a single pan-betacoronavirus vaccine to protect against three highly pathogenic human coronaviruses spanning two betacoronavirus subgenera.

immunology↗

bioRxiv2023

Stimulus novelty uncovers coding diversity in visual cortical circuits

Detecting novel stimuli in the environment is critical for learning and survival, yet the neural basis of novelty processing is not understood. To characterize cell type-specific novelty processing, we surveyed the activity of [~]15,000 excitatory and inhibitory neurons in mice performing a visual task with novel and familiar stimuli. Clustering revealed a dozen functional neuron types defined by experience-dependent encoding. Vasoactive-intestinal-peptide (Vip) expressing inhibitory neurons were diverse, encoding novel stimuli, omissions of familiar stimuli, or behavioral features. Distinct Somatostatin (Sst) expressing inhibitory neurons encoded either familiar or novel stimuli. Subsets of excitatory neurons co-clustered with specific Vip or Sst subpopulations, while Sst and Vip inhibitory clusters were non-overlapping. This study establishes that novelty processing is mediated by diverse functional neuron types in the visual cortex.

neuroscience↗

bioRxiv2022

Mutation-Guided Vaccine Design: A Strategy for Developing Boosting Immunogens for HIV Broadly Neutralizing Antibody Induction

A major goal of HIV-1 vaccine development is induction of broadly neutralizing antibodies (bnAbs). While success has been achieved in initiating bnAb B cell lineages, design of boosting immunogens that select for bnAb B cell receptors with improbable mutations required for bnAb affinity maturation remains difficult. Here we demonstrate a process for designing boosting immunogens for a V3-glycan bnAb B cell lineage. The immunogens induced affinity-matured antibodies by selecting for functional improbable mutations in bnAb precursor knock-in mice. Moreover, we show similar success in prime and boosting with nucleoside-modified mRNA-encoded HIV-1 envelope trimer immunogens, with improved selection by mRNA immunogens of improbable mutations required for bnAb binding to key envelope glycans. These results demonstrate the ability of both protein and mRNA prime-boost immunogens for selection of rare B cell lineage intermediates with neutralizing breadth after bnAb precursor expansion, a key proof-of concept and milestone towards development of an HIV vaccine. One-Sentence SummaryA vaccine strategy for selecting key rare antibody mutations is shown to induce HIV broadly neutralizing antibodies in mice.

immunology↗

bioRxiv2020

A new pathway for forming acetate and synthesizing ATP during fermentation in bacteria

Many bacteria and other organisms form acetate during fermentation. Forming acetate from high energy-precursors (acetyl-CoA or acetyl phosphate) is one of the few ways that fermentative bacteria generate ATP. Here we found a biochemical pathway for forming acetate and synthesizing ATP that was unknown in bacteria. We found the bacterium Cutibacterium granulosum formed acetate during fermentation of glucose. With enzymatic assays, we showed it formed acetate using a pathway involving two enzymes. The first enzyme, succinyl-CoA:acetate CoA-transferase (SCACT), forms acetate from acetyl-CoA. The second enzyme, succinyl-CoA synthetase (SCS), synthesizes ATP. This pathway is common in eukaryotes, but it has not been found in bacteria or other organisms. We found two related bacteria (C. acnes and Acidipropionibacterium acidipropionici) also used this pathway. None used the most common pathway for forming acetate in bacteria (involving acetate kinase and phosphotransacetylase). The SCACT/SCS pathway may be used by many bacteria, not just C. granulosum and relatives. When we searched genomes for bacteria known to form acetate, we found over 1/6 encoded this pathway. These bacteria belong to 104 different species and subspecies in 12 different phyla. With this discovery, all five pathways known to form acetate and ATP during fermentation can be found in bacteria. This discovery is important to manipulating fermentation and to the evolution of biochemical pathways.

biochemistry↗

bioRxiv2020

Characterizing the Human Heart Rate Circadian Pacemaker through Widely Available Wearable Devices

The effects of real-world stimuli and how they vary across individuals remains largely unknown for lack of a continuous real-world circadian marker. Here, we show how an underlying circadian rhythm in heart rate (CRHR) can be extracted from several widely used wearables. Analysis of over 130,000 days of data from medical interns on rotating shifts shows how CRHR dynamics are distinct from those of sleep-wake timing and vary greatly among individuals. Analysis of circadian timekeeping in travelers in 5 continents shows how the circadian timekeeping more carefully controls wake time rather than sleep time. We determine a personalized phase response curve (PRC) of CRHR to activity for each individual, representing the first passive and personalized determination of how human circadian timekeeping continuously changes due to real-world stimuli. These results collectively establish CRHR as a practical method to study circadian rhythms in the real world. eTOC BlurbWe show how the circadian rhythm in heart rate can be extracted from real world data collected by wearables. Studying data from a large cohort of medical interns working on shifts, we find very interesting dynamics of this circadian rhythm that are independent of the acute effects of activity or sleep-wake timing. These techniques can also determine personalized parameters of circadian timekeeping.

systems biology↗

bioRxiv2020

Analyzing Presymptomatic Tissue to Gain Insights into the Molecular and Mechanistic Origins of Late-Onset Degenerative Trinucleotide Repeat Disease

How genetic defects trigger the molecular changes that cause late-onset disease is important for understanding disease progression and therapeutic development. Fuchs endothelial corneal dystrophy (FECD) is an RNA-mediated disease caused by a trinucleotide CUG expansion in an intron within the TCF4 gene. The mutant intronic CUG RNA is present at 1-2 copies per cell, posing a challenge to understand how a rare RNA can cause disease. Late-onset FECD is a uniquely advantageous model for studying how RNA triggers disease because; 1) Affected tissue is routinely removed during surgery; 2) The expanded CUG mutation is one of the most prevalent disease-causing mutations, making it possible to obtain pre-symptomatic tissue from eye bank donors to probe how gene expression changes precede disease; and 3) The affected tissue is a homogeneous single cell monolayer, facilitating accurate transcriptome analysis. Here we use RNA sequencing (RNAseq) to compare tissue from individuals who are pre-symptomatic (Pre_S) to tissue from patients with late stage FECD (FECD_REP). The abundance of mutant repeat intronic RNA in Pre_S and FECD_REP tissue is elevated due to increased half-life in a corneal cell-specific manner. In Pre_S tissue, changes in splicing and extracellular matrix gene expression foreshadow the changes observed in advanced disease and predict the activation of the fibrosis pathway and immune system seen in late-stage patients. The absolute magnitude of splicing changes is similar in presymptomatic and late stage tissue. Our data identify gene candidates for early drivers of disease and biomarkers that may represent diagnostic and therapeutic targets for FECD. We conclude that changes in alternative splicing and gene expression are observable decades prior to the diagnosis of late-onset trinucleotide repeat disease.

molecular biology↗

bioRxiv2018

Detection of arterial wall abnormalities via Bayesian model selection

Patient-specific modeling of hemodynamics in arterial networks has so far relied on parameter estimation for inexpensive or small-scale models. We describe here a Bayesian uncertainty quantification framework which makes two major advances: an efficient parallel implementation, allowing parameter estimation for more complex forward models, and a system for practical model selection, allowing evidence-based comparison between distinct physical models. We demonstrate the proposed methodology by generating simulated noisy flow velocity data from a branching arterial tree model in which a structural defect is introduced at an unknown location; our approach is shown to accurately locate the abnormality and estimate its physical properties even in the presence of significant observational and systemic error. As the method readily admits real data, it shows great potential in patient-specific parameter fitting for hemodynamical flow models.

bioengineering↗

bioRxiv2017

EMHP: An accurate automated hole masking algorithm for single-particle cryo-EM image processing

1. Introduction 1. Introduction 2. Software Package Overview 3. Conclusions Funding References The recent surge in popularity of single-particle cryo-EM as a tool for molecular structure determination alongside advances in software that have reduced the computational infrastructure needed to process single-particle datasets (Kimanius et al, 2016) have created the need for a more streamlined suite of tools to locally facilitate initial data treatment and make processing more attainable at the workstation level.\n\nCurrent technical limitations inherent to the process of structure determination via single-particle cryo-EM require collecting very large data sets - often several thousands of images. This task is facilitated by automated imaging software, however downstream preprocessing steps such as quality asses ...

bioinformatics↗