Biology subjects

Kelley, C.

Publications and source records attributed to Kelley, C..

12 recordsLinked to original sources

bioRxiv2026

Behavioral state-dependent norepinephrine dynamics in the primary somatosensory and prefrontal cortices during tactile detection tasks

Animals must integrate sensory information, ignore behaviorally irrelevant stimuli, and respond to behaviorally relevant stimuli to find food, find mates, avoid predators, and ultimately survive. In mammals, these goal-directed behaviors require the coordinated activity of many brain regions, including sensory and prefrontal cortices and neuromodulatory brainstem nuclei like the locus coeruleus (LC), which is the brains primary source of norepinephrine (NE). NE release resulting from LC activity and arousal indexed by pupil size exert strong influences on goal-directed behavior. We explored the relationships between pupil size, cortical noradrenergic dynamics, and behavior in a tactile signal detection task. We monitored pupil dynamics and fluorescent GRABNE signals in somatosensory and medial prefrontal cortices simultaneously during task execution and found that pupil size and synchronization of GRABNE signals at baseline were strong predictors of whether animals chose to respond. Baseline and post-reward cortical GRABNE levels varied strongly with pupil-linked arousal. We also employed a generalized linear model - hidden Markov model (GLM-HMM) framework to identify distinct, stable behavioral states throughout the task that characterize task performance. We found distinct psychometric curves, task-related pupil dynamics, and cortical NE dynamics across these behavioral states. Significance StatementBehavioral state strongly shapes goal-directed behavior, which in turn depends on the coordinated activity of distributed brain regions, including the sensory and prefrontal cortices. By simultaneously measuring pupil size and cortical noradrenergic dynamics, and by identifying psychophysically distinct behavioral states during a tactile detection task, this study establishes links between pupil-linked arousal, norepinephrine signaling in somatosensory and prefrontal cortices, and trial outcomes. These findings provide new insight into how the locus coeruleus - norepinephrine system regulates perception and decision-making.

neuroscience↗

bioRxiv2025

Cell-line specific role of Cathepsin B in triple-negative breast cancer growth, invasion and response to chemotherapy

Cathepsins are papain-family cysteine proteases known to play a cell-intrinsic role in protein degradation in the lysosome, as well as in digesting ECM and surface proteins after being secreted. Both of these functions are known to mediate pro-tumorigenic effects of CTSB in a range of cancers. Here, we specifically investigate the role of CTSB in TNBC, an aggressive subtype of breast cancer, where we find that high expression of CTSB in TNBC is associated with better outcomes. We used CRISPR to knockout CTSB in two highly metastatic TNBC cell lines, MDA-MB-231 and MDA-MB-468, and find different effects. In MDA-MB-231 cells, knockout of CTSB has no effect on cell viability, increases tumor cell 3D invasion in an ECM-independent manner, and increases sensitivity to many standard of care chemotherapy drugs. However, in MDA-MB-468 cells, knockout of CTSB increases cell viability, decreases tumor cell 3D invasion, in an ECM-independent manner, and drives resistance to certain chemotherapy drugs without affecting response to others. We find that in these cells, CTSB is not secreted, and that differential downstream mTOR and Akt activation can explain the differences seen in these phenotypes. Overall, our studies demonstrate that CTSB can regulate TNBC cell phenotypes via its lysosomal cell-intrinsic role, but that effects are cell-line specific, suggesting potential heterogeneity in the role of CTSB in TNBC.

cancer biology↗

bioRxiv2025

p53Y220C-BET-bifunctionals (tPRIMEs) drive p53Y220C-mutant cancer cells into apoptosis

The transcription factor and tumor suppressor p53 is one of the most frequently mutated genes in cancer and has been difficult to target therapeutically due to its intrinsically disordered regions. The hotspot mutation p53Y220C, a mutation thermodynamically destabilizing p53, creates a unique extended crevice on the surface of the protein for which chemical matter has been identified over the last years. Advanced p53Y220C stabilizers reconstitute p53Y220C to its wildtype conformation, thereby restoring p53s role in target gene expression and inhibiting the growth of p53Y220C mutant cancer cell lines. We hypothesized that direct recruitment of the transcriptional elongation machinery to p53Y220C and its target genes may potentiate effects beyond p53 protein stabilization alone. We leveraged induced proximity to discover bifunctional molecules, p53Y220C-targeted PRoximity Induced Modulators of Expression (tPRIMEs), that specifically recognize the BET bromodomain proteins and induce stable ternary complexes with p53Y220C. p53Y220C-tPRIMEs potently inhibit proliferation and induce apoptosis of p53Y220C mutant cancer cell lines to a greater extent than the parental ligands alone or in combination. Gene expression analyses revealed that p53Y220C-tPRIMEs induce an increase in p53 target gene expression compared to parental binders. The superior antiproliferative activity, enhanced apoptosis, and increased p53 target gene expression are dependent on ternary complex formation. These data strongly suggest that a p53Y220C-tPRIME-mediated induced proximity approach between transcriptional regulators and p53Y220C - in contrast to p53 stabilization alone - can modulate the cell fate control from cell cycle inhibition to an apoptotic response, providing a compelling therapeutic modality for p53 mutant cancers.

cancer biology↗

bioRxiv2025

Integrative Structure of Norovirus NS3 Suggests a Role in RNA Transport

Human noroviruses (HuNoVs) are the leading global cause of non-bacterial gastroenteritis, yet no vaccines or antiviral therapies are currently approved1. The viral non-structural protein NS3 is a membrane-bound AAA+ ATPase of superfamily 3 (SF3) with multiple proposed roles in the norovirus replication cycle. However, the structure of NS3, and the mechanisms by which it contributes to genome replication and membrane remodeling, have remained unknown. We engineered a soluble, hexameric, and catalytically active form of NS3 and determined its cryo-EM structure in the presence of a nucleotide analogue at 2.9 [A] resolution. The structure adopts a split lock-washer architecture characteristic of AAA+ motors that operate via a hand-over-hand translocation mechanism2. Modeling of the nucleotide-binding site reveals conserved features governing ATP binding and hydrolysis. Using integrative modeling with AlphaFold3, we generated a full-length, membrane-associated model of NS3, in which an N-terminal transmembrane domain, central helical bundle, and AAA+ motor form a continuous conduit. This model supports a role for NS3 as a candidate membrane-spanning RNA translocase that couples ATP hydrolysis to genome movement. This structural framework helps address long-standing gaps in our understanding of norovirus replication and establishes a basis for mechanistic studies and structure-guided antiviral design.

microbiology↗

bioRxiv2025

Alpha modulation of spiking activity across multiple brain regions in mice performing a tactile selective detection task

Many cognitive and sensory processes are characterized by strong relationships between the timing of neuronal spiking and the phase of ongoing local field potential oscillations. The coupling of neuronal spiking in neocortex to the phase of alpha oscillations (8-12 Hz) has been well studied in nonhuman primates but remains largely unexplored in other mammals. How this alpha modulation of spiking differs between brain areas and cell types, as well as its role in sensory processing and decision making, are not well understood. We used Neuropixels 1.0 probes to chronically record neural activity from somatosensory cortex, prefrontal cortex, striatum, and amygdala in mice performing a whisker-based selective detection task. We observed strong spontaneous alpha modulation of single-neuron spiking activity during inter-trial intervals while mice performed the task. The prevalence and strength of alpha phase modulation differed significantly across regions and between cell types. Phase modulated neurons exhibited stronger responses to both go and no-go stimuli, as well as stronger motor- and reward-related changes in firing rate, than their unmodulated counterparts. The increased responsiveness of phase modulated neurons suggests they are innervated by more diverse populations. Alpha modulation of neuronal spiking during baseline activity also correlated with task performance. In particular, many neurons exhibited strong alpha modulation before correct trials, but not before incorrect trials. These data suggest that dysregulation of spiking activity with respect to alpha oscillations may characterize lapses in attention.

neuroscience↗

bioRxiv2023

Neuronal phase shifts differ for excitation vs. inhibition: a computer modeling study

Rhythmic activity is ubiquitous in neural systems, and impedance analysis has been widely used to examine frequency-dependent responses of neuronal membranes to rhythmic inputs. Impedance analysis assumes the neuronal membrane is a linear system, requiring the use of small signals to stay in a near-linear regime. However, postsynaptic potentials are often large and trigger nonlinear mechanisms. We therefore augmented impedance analysis to evaluate membrane responses in this nonlinear domain, analyzing responses to injected current for subthreshold membrane voltage (Vmemb), suprathreshold spike-blocked Vmemb, and spiking in a validated neocortical pyramidal neuron computer model. Responses in these output regimes were asymmetrical, with different phase shifts during hyperpolarizing and depolarizing half-cycles. Suprathreshold chirp stimulation gave equivocal results due to nonstationarity of response, requiring us to use fixed-frequency sinusoids. Sinusoidal inputs produced phase retreat: action potentials occurred progressively later in cycles of the input stimulus, resulting from adaptation. Conversely, sinusoidal current with increasing amplitude over cycles produced a pattern of phase advance: action potentials occurred progressively earlier. Phase retreat was dependent on Ih and IAHP currents; phase advance was modulated by these currents. Our results suggest differential responses of cortical neurons depending on the frequency of oscillatory input in the delta - beta range, which will play a role in neuronal responses to shifts in network state. We hypothesize that intrinsic cellular properties complement network properties and contribute to in vivo phase-shift phenomena such as phase precession, seen in place and grid cells, and phase roll, observed in hippocampal CA1 neurons. New & NoteworthyWe augmented electrical impedance analysis to characterize phase shifts between large amplitude current stimuli and nonlinear, asymmetric membrane potential responses. We predict different frequency-dependent phase shifts in response excitation versus inhibition, as well as shifts in spike timing over multiple input cycles, in resonant pyramidal neurons. We hypothesize that these effects contribute to navigation-related phenomena like phase precession and phase roll. Our neuron-level hypothesis complements, rather than falsifies, prior network-level explanations of these phenomena.

neuroscience↗

bioRxiv2022

Multiscale computer modeling of spreading depolarization in brain slices

Spreading depolarization (SD) is a slow-moving wave of neuronal depolarization accompanied by a breakdown of ion concentration homeostasis, followed by long periods of neuronal silence (spreading depression), and associated with several neurological conditions. We developed multiscale (ions to tissue slice) computer models of SD in brain slices using the NEURON simulator: 36,000 neurons (2 voltage-gated ion channels; 3 leak channels; 3 ion exchangers/pumps) in the extracellular space (ECS) of a slice (1 mm sides, varying thickness) with ion (K+, Cl-, Na+) and O2 diffusion and equilibration with a surrounding bath. Glia and neurons cleared K+ from the ECS via Na+/K+ pumps. SD propagated through the slices at realistic speeds of 2-4 mm/min, which increased by as much as 50% in models incorporating the effects of hypoxia or propionate. In both cases, the speedup was mediated principally by ECS shrinkage. Our model allows us to make testable predictions, including: 1. SD can be inhibited by enlarging ECS volume; 2. SD velocity will be greater in areas with greater neuronal density, total neuronal volume, or larger/more dendrites; 3. SD is all-or-none: initiating K+ bolus properties have little impact on SD speed; 4. Slice thickness influences SD due to relative hypoxia in the slice core, exacerbated by SD in a pathological cycle; 5. SD and high neuronal spike rates will be observed in the core of the slice. Cells in the periphery of the slice near an oxygenated bath will resist SD. SignificanceSpreading depolarization (SD) is a slow moving wave of electrical and ionic imbalances in brain tissue and is a hallmark of several neurological disorders. We developed a multiscale computer model of brain slices with realistic neuronal densities, ions, and oxygenation. Our model shows that SD is exacerbated by and causes hypoxia, resulting in strong SD dependence on slice thickness. Our model also predicts that the velocity of SD propagation is not dependent on its initiation, but instead on tissue properties, including the amount of extracellular space and the total area of neuronal membrane, suggesting faster SD following ischemic stroke or traumatic brain injury.

neuroscience↗

bioRxiv2021

Differential Vulnerability of Anterior Cingulate Cortex Cell-Types to Diseases and Drugs

In psychiatric disorders, mismatches between disease-states and therapeutic strategies are highly pronounced, largely because of unanswered questions regarding specific vulnerabilities of different cell-types and therapeutic responses. Which cellular events (housekeeping or salient) are most affected? Which cell-types succumb first to challenges, and which exhibit the strongest response to drugs? Are these events coordinated between cell-types? How does the disease-state and drug affect this coordination? To address these questions, we analyzed single-nucleus-RNAseq (sn-RNAseq) data from the human anterior cingulate cortex--a region involved in many psychiatric disorders. Density index, a metric for quantifying similarities and dissimilarities across functional profiles, was employed to identify common (housekeeping) or salient functional themes across all cell-types. Cell-specific signatures were integrated with existing disease and drug-specific signatures to determine cell-type-specific vulnerabilities, druggabilities, and responsiveness. Clustering of functional profiles revealed cell-types jointly participating in these events. SST and VIP interneurons were found to be most vulnerable, whereas pyramidal neurons were least vulnerable. Overall, the disease-state is superficial layer-centric, largely influences cell-specific salient themes, strongly impacts disinhibitory neurons, and influences astrocyte interaction with a subset of deep-layer pyramidal neurons. Drug activities, on the other hand, are deep layer-centric and involve activating a distinct subset of deep-layer pyramidal neurons to circumvent the disinhibitory circuit malfunctioning in the disease-state. These findings demonstrate a novel application of sn-RNAseq data to explain drug and disease action at a systems level, suggests a targeted drug development and reevaluate various postmortem-based findings.

neuroscience↗

bioRxiv2021

Chronic and progressive deficits after a single closed head injury in mice

BackgroundAcute injury following brain trauma may evolve into a chronic and progressive disorder. Chronic consequences of TBI have been understudied, in part, due to the lack of robust behavioral changes that are delayed in onset as well as chronic and progressive. Assessment of the chronic consequences of TBI also must distinguish behavioral changes that arises due to age vs those that develop and evolve over time due to injury. MethodsC57BL/6 mice receive single closed head injury (CHI) and are analyzed at 7DPI, 14DPI or 180DPI on neurological severity score, open field, rotarod, beam walk, and simple-complex wheel. ResultsIn the center of open field, injured mice have a turn bias at 180 days post-injury (DPI) not present at 7DPI. On rotarod, injured mice have shorter latencies at 7DPI, but not at 180DPI due to a large age effect in sham-injured mice. On beam walk at 180DPI, both sham and injured groups more slowly traverse a 2cm and 1cm beam than at 7DPI. Foot-faults show no significant effects of age or injury. On simple wheel injury affects speed at 14DPI with no effect on distance travelled. The lack of injury-dependent effects on beam walk or simple-complex wheel despite visible impairment was the impetus to assess limb position using Deeplabcut markerless tracking. Custom Python scripts were then developed to compute beam walk absition or foot fault severity (integral of limb displacement over time), and step frequency and quadrupedal limb coordination in simple-complex wheel. On the 2cm beam, age increased absition in all limbs of uninjured mice and both forelimbs of injured mice. On the 1cm beam both forelimbs and the left hindlimb of injured mice at 180DPI have larger absition than uninjured mice at 180DPI or injured mice at 7DPI. On a simple wheel injury affected speed only at 14 DPI with no effect on distance travelled. In contrast, injured mice at 180DPI developed a compensatory running strategy by increasing step frequency variability. This allowed injured mice at 180 DPI to reach sham-level quadrupedal limb coordination and improve running speed as compared to 14 DPI assessment. On complex wheel, injured mice at 180DPI do not express this compensatory running strategy resulting in impaired quadrupedal limb coordination. These data suggest chronic and progressive motor deficits of injured mice at 180DPI. ConclusionsA single impact produces chronic and progressive motor deficits. Quantitative motor analysis using DeepLabCut tracking reveals deficits not seen using standard outcomes.

neuroscience↗

bioRxiv2021

Effects of Ih and TASK-like shunting current on dendritic impedance in layer 5 pyramidal-tract neurons

Pyramidal neurons in neocortex have complex input-output relationships that depend on their morphologies, ion channel distributions, and the nature of their inputs, but which cannot be replicated by simple integrate-and-fire models. The impedance properties of their dendritic arbors, such as resonance and phase shift, shape neuronal responses to synaptic inputs and provide intraneuronal functional maps reflecting their intrinsic dynamics and excitability. Experimental studies of dendritic impedance have shown that neocortical pyramidal tract neurons exhibit distance-dependent changes in resonance and impedance phase with respect to the soma. We therefore investigated how well several biophysically-detailed multi-compartment models of neocortical layer 5 pyramidal tract neurons reproduce the location-dependent impedance profiles observed experimentally. Each model tested here exhibited location-dependent impedance profiles, but most captured either the observed impedance amplitude or phase, not both. The only model that captured features from both incorporates HCN channels and a shunting current, like that produced by Twik-related acid-sensitive K+(TASK) channels. TASK-like channel activity in this model was dependent on local peak HCN channel conductance (Ih). We found that while this shunting current alone is insufficient to produce resonance or realistic phase response, it modulates all features of dendritic impedance, including resonance frequencies, resonance strength, synchronous frequencies, and total inductive phase. We also explored how the interaction of Ih and a TASK-like shunting current shape synaptic potentials and produce degeneracy in dendritic impedance profiles, wherein different combinations of Ih and shunting current can produce the same impedance profile. New & NoteworthyWe simulated chirp current stimulation in the apical dendrites of 5 biophysically-detailed multi-compartment models of neocortical pyramidal tract neurons and found that a combination of HCN channels and TASK-like channels produced the best fit to experimental measurements of dendritic impedance. We then explored how HCN and TASK-like channels can shape the dendritic impedance as well as the voltage response to synaptic currents.

neuroscience↗

bioRxiv2017

Zinc detoxification: a functional genomics and transcriptomics analysis in Drosophila melanogaster cultured cells

Cells require some metals, such as zinc and manganese, but excess levels of these metals can be toxic. As a result, cells have evolved complex mechanisms for maintaining metal homeostasis and surviving metal intoxication. Here, we present the results of a large-scale functional genomic screen in Drosophila cultured cells for modifiers of zinc chloride toxicity, together with transcriptomics data for wildtype or genetically zinc-sensitized cells challenged with mild zinc chloride supplementation. Altogether, we identified 47 genes for which knockdown conferred sensitivity or resistance to toxic zinc or manganese chloride treatment, and more than 1800 putative zinc-responsive genes. Analysis of the omics data points to the relevance of ion transporters, glutathione-related factors, and conserved disease-associated genes in zinc detoxification. Specific genes identified in the zinc screen include orthologs of human disease-associated genes CTNS, PTPRN (also known as IA-2), and ATP13A2 (also known as PARK9). We show that knockdown of red dog mine (rdog; CG11897), a candidate zinc detoxification gene encoding an ABCC-type transporter family protein related to yeast cadmium factor (YCF1), confers sensitivity to zinc intoxication in cultured cells and that rdog is transcriptionally up-regulated in response to zinc stress. As there are many links between the biology of zinc and other metals and human health, the omics datasets presented here provide a resource that will allow researchers to explore metal biology in the context of diverse health-relevant processes.

genetics↗

bioRxiv2017

Variable dose analysis: A novel RNAi-based method for detection of synthetic lethal interactions

Synthetic sick or synthetic lethal (SS/L) screens are a powerful way to identify candidate drug targets to specifically kill tumor cells but such screens generally suffer from low reproducibility. We found that many SS/L interactions involve essential genes and are therefore detectable within a limited range of knockdown efficiency. Such interactions are often missed by overly efficient RNAi reagents. We therefore developed an assay that measures viability over a range of knockdown efficiency within a cell population. This method, called variable dose analysis (VDA), is highly sensitive to viability phenotypes and reproducibly detects SS/L interactions. We applied the VDA method to search for SS/L interactions with TSC1 and TSC2, the two tumor suppressors underlying tuberous sclerosis complex (TSC) and generated a SS/L network for TSC. Using this network, we identified four FDA-approved drugs that selectively affect viability of TSC deficient cells, representing promising candidates for repurposing to treat TSC-related tumors.

cancer biology↗