Biology subjects

Keller, K.

Publications and source records attributed to Keller, K..

15 recordsLinked to original sources

bioRxiv2026

Transcriptomic profiling of normal and glaucomatous trabecular meshwork cells in a tissue-like soft ECM environment

Purpose. Trabecular meshwork (TM) dysfunction contributes to the elevated intraocular pressure in primary open-angle glaucoma. To better understand the molecular signature distinguishing glaucomatous from normal TM cells, we interrogated their genome-wide transcriptomic differences in a tissue-like soft extracellular matrix (ECM) microenvironment. Methods. Primary human glaucomatous and normal TM cell strains (N = 5 each) from three independent laboratories were plated on bioengineered collagen type I/hyaluronic acid/elastin-like polypeptide ECM hydrogels in 10% FBS media for 4-5 days, then serum-free media for 2 days. Cell-laden hydrogels were homogenized in TRIzol for RNA isolation, quality assessment, and library preparation, followed by paired-end 100-bp Illumina sequencing. Differential expression was assessed using DESeq2, including glaucoma status, originating laboratory, and donor age/sex in the model. Differentially expressed genes (DEGs) were defined as p < 0.05 and |fold change| [≥] 2, followed by Gene Ontology (GO) enrichment and QIAGEN Ingenuity Pathway Analysis (IPA). Results. In total, 588 DEGs distinguished the glaucomatous from the normal TM transcriptome (393 up-regulated in glaucomatous TM; 195 up-regulated in normal TM, i.e., down-regulated in glaucomatous TM). GO and IPA causal analyses revealed three coordinated disease programs: (i) TGF-{beta}/Wnt-driven ECM remodeling and fibrosis, (ii) NF-{kappa}B-associated inflammation, and (iii) a hypoxia/metabolic-stress program linked to p300/CREBBP chromatin co-activation. Conclusions. These data define a transcriptomic signature of glaucomatous TM cells when cultured in a soft physiologic ECM microenvironment, independent of the originating laboratory, with three mechanistic axes (ECM/fibrosis, inflammation, hypoxia/metabolism), and nominate p300 (encoded by EP300) as a candidate upstream node integrating these programs.

cell biology↗

bioRxiv2026

A cargo receptor entrapment complex is a therapeutic node for genetically and clinically distinct proteinopathies

Severe proteinopathies--such as retinitis pigmentosa, a form of inherited blindness--are driven by genetic mutations that overwhelm the quality control of the post-endoplasmic reticulum (post-ER) secretory pathway, causing toxic protein accumulation. Here, we identify a therapeutic node defined by a hetero-oligomeric cargo receptor complex consisting of TMED7, 2, 9, and 10. This "entrapment complex" anchors structurally and functionally diverse mutant clients within the early secretory pathway via TMED7 binding to the integral Golgi protein GRASP55. Disruption of the entrapment complex results in the clearance of accumulated protein cargoes. In vivo ablation of the entrapment node via inducible genetic deletion or via the small molecule BRD7635 reverses histopathological hallmarks and rescues functional deficits in clinically distinct proteinopathies of the kidney and the eye, including mitigating vision loss in a mouse model of retinitis pigmentosa.

cell biology↗

bioRxiv2026

Predicting driver distraction using a single channel ear EEG

Cognitive distraction poses a major risk to driving safety, yet remains difficult to detect in real time because it often lacks overt behavioral markers. Neurophysiological measures such as electroencephalography (EEG) provide objective indices of cognitive load, but conventional EEG systems are impractical for real-world deployment due to their intrusiveness and computational demands. The present study examined whether cognitive distraction during naturalistic driving can be decoded using a single-channel, non-invasive in-ear EEG, and how its temporal dynamics compare with those obtained from full-cap scalp EEG and behavioral measures. Twenty-seven participants performed a dual-task paradigm in a highly immersive driving simulator, combining continuous vehicle control with low- and high-load arithmetic tasks presented on an in-vehicle display. Single-channel in-ear EEG, 24-channel scalp EEG, eye movements, and head rotation were recorded concurrently. Time-resolved multivariate pattern analysis was applied to decode working-memory load with millisecond precision across modalities. Cognitive distraction was reliably decoded from in-ear EEG, with detection latency and temporal generalization profiles closely matching those of full-cap scalp EEG. Although peak decoding performance was higher for scalp EEG, the timing and temporal stability of distraction-related neural signatures were largely overlapping between the two neural modalities. Eye velocity provided the earliest and most sensitive behavioral marker of distraction, while head rotation contributed complementary but weaker information. Scalp EEG topographies indicated that neural signals underlying decoding were closely linked to oculomotor and visuomotor processes engaged during task performance. These findings demonstrate that single-channel in-ear EEG provides a temporally precise and low-burden neural marker of cognitive distraction during driving. By prioritizing early detection and minimal hardware over maximal classification accuracy, the results identify a practical operating point for wearable EEG-based driver monitoring systems and support the feasibility of fast, off-the-shelf decoding approaches for real-world applications.

neuroscience↗

bioRxiv2025

Ecological cues orchestrate concerted courtship in a Drosophila host specialist

Mating decisions are often attributed to the sensory signaling between prospective sexual partners. Yet these interactions are also shaped by the broader environmental context in which they unfold, to appropriately align sexual arousal with reproductive opportunities. Here we show that in the host specialist Drosophila erecta mating is strictly contingent on the ecological and social environment generated as flies densely aggregate in groups on a food patch. We find that food volatiles directly promote male sexual arousal, triggering individuals to sample and pursue potential mates, giving rise to dynamic interactions across the group. The ensuing visual motion transforms each males visual field, which in turn further amplifies his arousal, generating a multisensory feedback loop that coordinately promotes courtship across individuals. D. erectas strict dependence on environmental cues appears latent in related species, such as D. melanogaster, where food odor can promote arousal but is dispensable for vigorous courtship. Comparative circuit analyses reveal that species-specific thresholds for sexual arousal reflect variation in how olfactory input modulates conserved nodes controlling courtship drive, rendering food volatiles a strict sensory gate only in D. erecta. Together, our findings highlight how ecological cues not directly tied to sexual signaling can profoundly influence reproductive behavior and reorganize the social landscape to ensure mating occurs in contexts where reproductive opportunities are abundant.

neuroscience↗

bioRxiv2025

The neuro-ocular costs of texting during driving

Texting while driving is among the most dangerous forms of distraction, yet the neurophysiological mechanisms linking cognitive load, gaze control, and driving behavior remain poorly understood. Here, EEG, eye tracking, head kinematics, and driving performance were recorded in a naturalistic driving task while participants solved arithmetic problems presented on a dashboard-mounted display under low and high working-memory (WM) load, mimicking real-world interaction with dashboard media. High WM load resulted in slower reaction times, reduced accuracy, prolonged gaze toward the stimulus, increased corrective head rotations, and compensatory reductions in driving speed. Time-frequency analysis revealed robust alpha power suppression ([~]8-13 Hz) over occipito-parietal regions scaling with WM load and closely paralleling gaze behavior. Source reconstruction further identified a transient, stimulus-locked increase in oscillatory power at [~]15 Hz involving the ipsilateral cerebellum and posterior parietal preceding the head rotation onset. These findings illuminate the time course of a neuro-ocular action circuit involving cerebellum and cortex as candidate neurophysiological precursor of upcoming behavioral costs as a result of driver distraction. Bridging cognitive neuroscience and applied traffic research, the present results provide an ecologically valid framework for studying action-attention coupling in real-world behavior.

neuroscience↗

bioRxiv2025

Strain variation identifies a neural substrate for behavioral evolution in Drosophila

Sexual selection acts on heritable differences within species, driving the parallel diversification of signal production in one sex and behavioral responses in the other. This coevolution implies that sensory preferences are themselves variable traits, yet the neural basis of such variation remains unclear. Here, we identify striking strain-specific differences in Drosophila melanogaster male mate preferences that arise from differential sensitivity to heterospecific female pheromones. We map this variation to an ascending inhibitory pathway targeting a central circuit node known to dynamically pattern courtship. Inhibitory circuits thus emerge as a key locus for shaping mate discrimination via transient suppression of a males pursuit. Our findings highlight how variation within sensory circuitry serves as a substrate for selection, fueling the evolution of reproductive barriers between species.

neuroscience↗

bioRxiv2024

Released Bacterial ATP Shapes Local and Systemic Inflammation during Abdominal Sepsis

Sepsis causes millions of deaths per year worldwide and is a current global health priority declared by the WHO. Sepsis-related deaths are a result of dysregulated inflammatory immune responses indicating the need to develop strategies to target inflammation. An important mediator of inflammation is extracellular adenosine triphosphate (ATP) that is secreted by inflamed host cells and tissues, and also by bacteria in a strain-specific and growth phase-dependent manner. Here, we investigated the mechanisms by which bacteria release ATP. Using genetic mutant strains of Escherichia coli (E. coli), we demonstrate that ATP release is dependent on ATP synthase within the inner bacterial membrane. In addition, impaired integrity of the outer bacterial membrane and bacterial death notably contribute to ATP release. In a mouse model of abdominal sepsis, local effects of bacterial ATP were analysed using a transformed E. coli bearing an arabinose-inducible periplasmic apyrase hydrolyzing ATP to be released. Abrogating bacterial ATP release shows that bacterial ATP suppresses local immune responses, resulting in reduced neutrophil counts and impaired survival. In addition, bacterial ATP has systemic effects via its transport in outer membrane vesicles (OMV). ATP-loaded OMV are quickly distributed throughout the body and upregulated expression of genes activating degranulation in neutrophils, potentially contributing to the exacerbation of sepsis severity. This study reveals mechanisms of bacterial ATP release and its local and systemic roles in sepsis pathogenesis.

microbiology↗

bioRxiv2023

Noise-induced changes in rat head stability and orientation correlate with dysfunction of otolith irregular afferents

Exposure to intense noise damages both the cochlea and vestibular end organs. Our group previously reported attenuated vestibular short-latency evoked potentials (VsEP) and reduced numbers of calretinin-positive (CR+) calyces in the saccule following noise exposure. Here, we examined rats resting head orientation with respect to gravity as well as head stability following a 4-hour exposure to 120 dB SPL noise. We also assessed how behavioral changes are related to changes in VsEP waveforms and calretinin expression in the utricle and saccule to elucidate potential underlying mechanisms. We found significant reductions in the P2N2 and N2P3 amplitudes following noise exposure. The number of CR+ calyces in both saccule and utricle were also significantly reduced. The size of the reduction in N2P3 amplitude was significantly correlated to the number of CR+ calyces. Animals with a greater loss of CR+ calyces in the utricle following noise showed significant decreases in the average speed of y-axis rotational head motion, while those with a fewer loss of CR+ calyces showed significant increases. In addition, animals with larger noise-induced changes in VsEP and CR+ calyces held their heads motionless longer following noise exposure. We hypothesize that noise exposure is inherently destructive to an animals head stability and thereby manifests as an increase in average head speed in mildly to moderately affected animals. But when the damage was large enough, animals exhibited reduced duration and head motion speed as a behavioral adaptation. The noise exposure also significantly altered the pitch angle of head orientation in animals who had the largest reduction in CR+ calyces in the saccule, suggesting that saccular irregular afferents, including those that are CR+, are critical in control of head and body posture.

neuroscience↗

bioRxiv2023

Characterization of extracellular matrix deposited by segmental trabecular meshwork cells

Biophysical and biochemical attributes of the extracellular matrix are major determinants of cell fate in homeostasis and disease. Ocular hypertension and glaucoma are diseases where the trabecular meshwork tissue responsible for aqueous humor egress becomes stiffer accompanied by changes in its matrisome in a segmental manner with regions of high or low flow. Prior studies demonstrate these alterations in the matrix are dynamic in response to age and pressure changes. The underlying reason for segmentation or differential response to pressure and stiffening are unknown. This is largely due to a lack of appropriate models (in vitro or ex vivo) to study this phenomena. In this study, we characterize the biomechanical attributes, matrisome, and incidence of crosslinks in the matrix deposited by primary cells isolated from segmental flow regions and when treated with glucocorticosteroid. Data demonstrate that matrix deposited by cells from low flow regions are stiffer and exhibit a greater number of immature and mature crosslinks, and that these are exacerbated in the presence of steroid. We also show a differential response of high or low flow cells to steroid via changes observed in the matrix composition. We conclude that although a mechanistic basis for matrix stiffness was undetermined in this study, it is a viable tool to study cell-matrix interactions and further our understanding of trabecular meshwork pathobiology.

cell biology↗

bioRxiv2022

Novel mtDNA Imparts the Connective Tissue Disorder of a Tourette Pedigree

Mitochondrial dysfunction is associated with a range of clinical manifestations including neuropsychiatric and metabolic disorder. Here, we reanalyzed a family with an L-Histidine Decarboxylase (HDC) variant previously linked to Tourette syndrome but with associated connective tissue and metabolic features of unknown etiology. We identified a mitochondrial haplogroup J-defining mutation on the haplogroup H background that functionally interacts with the L-Histidine Decarboxylase variant via calcium homeostasis. Our findings establish how a common mtDNA variant on a different mtDNA background can result in mitochondrial dysfunction, demonstrate a role for histaminergic signaling in modifying mitochondrial phenotypes, and link mitochondria dysfunction to connective tissue phenotypes.

genetics↗

bioRxiv2021

High Resolution Slide-seqV2 Spatial Transcriptomics Enables Discovery of Disease-Specific Cell Neighborhoods and Pathways

High resolution spatial transcriptomics is a transformative technology that enables mapping of RNA expression directly from intact tissue sections; however, its utility for the elucidation of disease processes and therapeutically actionable pathways remain largely unexplored. Here we applied Slide-seqV2 to mouse and human kidneys, in healthy and in distinct disease paradigms. First, we established the feasibility of Slide-seqV2 in human kidney by analyzing tissue from 9 distinct donors, which revealed a cell neighborhood centered around a population of LYVE1+ macrophages. Second, in a mouse model of diabetic kidney disease, we detected changes in the cellular organization of the spatially-restricted kidney filter and blood flow regulating apparatus. Third, in a mouse model of a toxic proteinopathy, we identified previously unknown, disease-specific cell neighborhoods centered around macrophages. In a spatially-restricted subpopulation of epithelial cells, we also found perturbations in 77 genes associated with the unfolded protein response (UPR). Our studies illustrate and experimentally validate the utility of Slide-seqV2 for the discovery of disease-specific cell neighborhoods. One-Sentence SummaryHigh resolution Slide-seqV2 spatial transcriptomics in human and mouse kidneys.

molecular biology↗

bioRxiv2021

Obesity-instructed TREM2high macrophages identified by comparative analysis of diabetic mouse and human kidney at single cell resolution

Mouse models are a tool for studying the mechanisms underlying complex diseases; however, differences between species pose a significant challenge for translating findings to patients. Here, we used single-cell transcriptomics and orthogonal validation approaches to provide cross-species taxonomies, identifying shared broad cell classes and unique granular cellular states, between mouse and human kidney. We generated cell atlases of the diabetic and obese kidney using two different mouse models, a high-fat diet (HFD) model and a genetic model (BTBR ob/ob), at multiple time points along disease progression. Importantly, we identified a previously unrecognized, expanding Trem2high macrophage population in kidneys of HFD mice that matched human TREM2high macrophages in obese patients. Taken together, our cross-species comparison highlights shared immune and metabolic cell-state changes.

genomics↗

bioRxiv2020

Candidate Explorer: a tool for discovery, evaluation, and display of mutations causing significant immune phenotypes

When applied to immunity, forward genetic studies use meiotic mapping to provide strong statistical evidence that a particular mutation is causative of a particular immune phenotype. Notwithstanding this, co-segregation of multiple mutations, occasional unawareness of mutations, and paucity of homozygotes may lead to erroneous declarations of cause and effect. We sought to improve the selection of authentic causative mutations using a machine learning software tool, Candidate Explorer (CE), which integrates 65 data features into a single numeric score, mathematically convertible to the likelihood of verification of any putative mutation-phenotype association. CE has identified most genes within which mutations can be causative of flow cytometric phenovariation in Mus musculus. The majority of these genes were not previously known to support immune function or homeostasis. Mouse geneticists will find CE data informative in identifying causative mutations within quantitative trait loci, while clinical geneticists may use CE to help connect causative variants with rare heritable diseases of immunity, even in the absence of linkage information. CE displays integrated mutation, phenotype, and linkage data, and is freely available for query online.

genetics↗

bioRxiv2020

A High Content Screen for Mucin-1-Reducing Compounds Identifies Fostamatinib as a Candidate for Rapid Repurposing for Acute Lung Injury during the COVID-19 pandemic

Drug repurposing is the only method capable of delivering treatments on the shortened time-scale required for patients afflicted with lung disease arising from SARS-CoV-2 infection. Mucin-1 (MUC1), a membrane-bound molecule expressed on the apical surfaces of most mucosal epithelial cells, is a biochemical marker whose elevated levels predict the development of acute lung injury (ALI) and respiratory distress syndrome (ARDS), and correlate with poor clinical outcomes. In response to the pandemic spread of SARS-CoV-2, we took advantage of a high content screen of 3,713 compounds at different stages of clinical development to identify FDA-approved compounds that reduce MUC1 protein abundance. Our screen identified Fostamatinib (R788), an inhibitor of spleen tyrosine kinase (SYK) approved for the treatment of chronic immune thrombocytopenia, as a repurposing candidate for the treatment of ALI. In vivo, Fostamatinib reduced MUC1 abundance in lung epithelial cells in a mouse model of ALI. In vitro, SYK inhibition by Fostamatinib promoted MUC1 removal from the cell surface. Our work reveals Fostamatinib as a repurposing drug candidate for ALI and provides the rationale for rapidly standing up clinical trials to test Fostamatinib efficacy in patients with COVID-19 lung injury.

cell biology↗

bioRxiv2020

RAAS blockade, kidney disease, and expression of ACE2, the entry receptor for SARS-CoV-2, in kidney epithelial and endothelial cells

SARS-CoV-2, the coronavirus that causes COVID-19, binds to angiotensin-converting enzyme 2 (ACE2) on human cells. Beyond the lung, COVID-19 impacts diverse tissues including the kidney. ACE2 is a key member of the Renin-Angiotensin-Aldosterone System (RAAS) which regulates blood pressure, largely through its effects on the kidney. RAAS blockers such as ACE inhibitors (ACEi) and Angiotensin Receptor Blockers (ARBs) are widely used therapies for hypertension, cardiovascular and chronic kidney diseases, and therefore, there is intense interest in their effect on ACE2 expression and its implications for SARS-CoV-2 pathogenicity. Here, we analyzed single-cell and single-nucleus RNA-seq of human kidney to interrogate the association of ACEi/ARB use with ACE2 expression in specific cell types. First, we performed an integrated analysis aggregating 176,421 cells across 49 donors, 8 studies and 8 centers, and adjusting for sex, age, donor and center effects, to assess the relationship of ACE2 with age and sex at baseline. We observed a statistically significant increase in ACE2 expression in tubular epithelial cells of the thin loop of Henle (tLoH) in males relative to females at younger ages, the trend reversing, and losing significance with older ages. ACE2 expression in tLoH increases with age in females, with an opposite, weak effect in males. In an independent cohort, we detected a statistically significant increase in ACE2 expression with ACEi/ARB use in epithelial cells of the proximal tubule and thick ascending limb, and endothelial cells, but the association was confounded in this small cohort by the underlying disease. Our study illuminates the dynamics of ACE2 expression in specific kidney cells, with implications for SARS-CoV-2 entry and pathogenicity.

genomics↗