Biology subjects

Kelly, M. J.

Publications and source records attributed to Kelly, M. J..

13 recordsLinked to original sources

bioRxiv2026

Identifying Novel Estrogenic Mitochondrial Targets in Hypothalamic Proopiomelanocortin Neurons by Chemoproteomics

Loss of estrogens at menopause is linked to impaired brain metabolism and increased risk of Alzheimers disease (AD). However, estrogen replacement therapies are limited due to the deleterious effects of estrogen on peripheral organs and increased risk of vascular dementia. We have developed a non-steroidal estrogenic compound, STX, which does not bind to the classical estrogen receptors and {beta}, but mimics estrogenic signaling in the central nervous system (CNS) without the peripheral reproductive actions. STX is protective against neurodegeneration in stroke and AD models, but its molecular targets are unknown. Here, we identified and validated STX neural targets using chemoproteomic, molecular biological, electrophysiological and metabolic assays of hypothalamic proopiomelanocortin (POMC) neurons. Chemoproteomic profiling identified voltage dependent anion channels (VDAC1-3) as major intracellular binding partners in mHypo43 (POMC) cells. Based on quantitative single-cell PCR, Vdac2 was identified as the dominant isoform in female hypothalamic POMC neurons. Seahorse metabolic flux analyses showed that STX potently increased glycolysis, oxidative respiration and mitochondrial ATP production in mHypo43 cells. Nanomolar concentrations of STX enhanced VDAC2 voltage-dependent gating in reconstituted lipid membranes and shifted the low-conductance states toward anion selectivity, consistent with increased ATP flux. Together, these findings reveal a mechanism for the neuroprotective effects of STX through enhancing mitochondrial bioenergetics and modulating VDAC channel properties, potentially increasing cellular energy stores. Therefore, this work identifies previously unrecognized estrogenic mitochondrial targets and provides a mechanistic basis for the neuroprotective actions of STX relevant to menopause-associated brain vulnerability.

neuroscience↗

bioRxiv2026

A Hybrid Physics-Deep Learning Framework for Combinatorial De Novo Design of Small-Molecule Binding Proteins

Engineering small-molecule binding proteins de novo remains a significant challenge as even advanced generative models struggle to model the atom-level details of protein-ligand interactions with sufficient accuracy. Higher experimental success rates have resulted from methods that explicitly scaffold predefined binding interactions into helical bundles. Here we introduce a scaffolding strategy that generalizes to alpha-beta architectures. By screening thousands of combinatorially assembled protein-ligand interactions against diverse de novo backbones with finely varied pocket geometries, the protocol allows for high-fidelity accommodation of target interaction geometries. Our protocol then integrates physics-based and deep learning methods for optimization of interfacial interactions and sequence-structure compatibility, considerably improving in silico design metrics. Applying this method to two chemically similar steroids achieved a notable experimental success rate (4/26 designs bind their targets), and NMR structures of two designs are in good agreement with design models. Our generalizable, atomically precise approach offers a robust framework for small-molecule binder design, effectively eliminating the need for high-throughput screening.

bioengineering↗

bioRxiv2025

Melanocortin-responsive Kiss1 neurons of the arcuate nucleus drive energy expenditure through glutamatergic signaling to the dorsomedial hypothalamus.

Energy expenditure (EE) is essential for metabolic homeostasis, yet its central regulation remains poorly understood. Here, we identify arcuate Kiss1 neurons as key regulators of EE in male mice. Ablation of these neurons induced obesity, while their chemogenetic activation increased brown adipose tissue (BAT) thermogenesis without affecting food intake. This action is mediated by glutamatergic projections from Kiss1ARC neurons to CART/Lepr-expressing neurons in the dorsomedial hypothalamus, which activate the raphe pallidus-BAT pathway. CRISPR-mediated deletion of the vesicular glutamate transporter 2 (Vglut2) from Kiss1ARC neurons replicated the obesogenic effect. Furthermore, deletion of the melanocortin 4 receptor (MC4R) from Kiss1 neurons resulted in obesity, reduced energy expenditure and impaired thermogenesis. Optogenetic stimulation of pro-opiomelanocortin (POMC) fibers evoked inward currents in Kiss1 neurons, that were attenuated by MC4R antagonism. Our findings reveal a previously unrecognized neural circuit that mediates melanocortin action on energy expenditure, offering new insights into central mechanisms of metabolic control.

neuroscience↗

bioRxiv2024

De novo design of proteins that bind naphthalenediimides, powerful photooxidants with tunable photophysical properties

De novo protein design provides a framework to test our understanding of protein function and to build proteins with cofactors and functions not found in nature. Here, we report the design of proteins designed to bind powerful photooxidants and the evaluation of the use of these proteins to generate diffusible small molecule reactive species for applications in proximity labeling. Because excited state dynamics are influenced by the dynamics and hydration of a photo-oxidants environment, it was important to not only design a binding site, but also to evaluate its dynamic properties. Thus, we used computational design in conjunction with molecular dynamics (MD) simulations to design a protein, designated NBP (NDI Binding Protein) that held a naphthalenediimide (NDI), a powerful photooxidant, in a programable molecular environment. Solution NMR confirmed the structure of the complex. We evaluated two NDI cofactors in this de novo protein, using ultra-fast pump-probe spectroscopy to evaluate light-triggered intra- and intermolecular electron transfer function. Moreover, we demonstrated the utility of this platform to activate multiple molecular probes for protein proximity labeling.

biophysics↗

bioRxiv2024

Inhibition of heme biosynthesis triggers cuproptosis in acute myeloid leukaemia.

The ubiquitous metabolite heme has diverse enzymatic and signalling functions in most mammalian cells. Cells can salvage heme from the extracellular environment or synthesise heme de novo from succinyl-CoA and glycine through a series of 8 enzymatic reactions catalysed by heme biosynthesis enzymes (HBEs) localised in the mitochondria and the cytosol1,2. Through integrated analyses of mouse models, human cell lines and primary patient samples, we identify de novo heme biosynthesis as a selective dependency in acute myeloid leukaemia (AML). The dependency is underpinned by a propensity of AML cells, and especially leukaemic stem cells (LSCs) to downregulate HBEs. The resultant low heme state upregulates self-renewal genes via the heme sensing transcription factor BACH1, but also places leukaemia cells on the threshold of heme starvation. Genetic or pharmacological inhibition of HBEs induces cuproptosis, a form of programmed cell death caused by copper accumulation and oligomerisation of lipoylated proteins3. Moreover, we identify pathways that are synthetic lethal with heme biosynthesis, including glycolysis, which can be leveraged for combination strategies. Altogether, our work uncovers a heme rheostat that controls gene expression and drug sensitivity in AML and implicates HBE inhibition as a novel cuproptosis trigger.

cancer biology↗

bioRxiv2024

Estradiol elicits distinct firing patterns in arcuate nucleus kisspeptin neurons of females through altering ion channel conductances

Hypothalamic kisspeptin (Kiss1) neurons are vital for pubertal development and reproduction. Arcuate nucleus Kiss1 (Kiss1ARH) neurons are responsible for the pulsatile release of Gonadotropin-releasing Hormone (GnRH). In females, the behavior of Kiss1ARH neurons, expressing Kiss1, Neurokinin B (NKB), and Dynorphin (Dyn), varies throughout the ovarian cycle. Studies indicate that 17{beta}-estradiol (E2) reduces peptide expression but increases Vglut2 mRNA and glutamate neurotransmission in these neurons, suggesting a shift from peptidergic to glutamatergic signaling. To investigate this shift, we combined transcriptomics, electrophysiology, and mathematical modeling. Our results demonstrate that E2 treatment upregulates the mRNA expression of voltage-activated calcium channels, elevating the whole-cell calcium current and that contribute to high-frequency burst firing. Additionally, E2 treatment decreased the mRNA levels of Canonical Transient Receptor Potential (TPRC) 5 and G protein-coupled K+ (GIRK) channels. When TRPC5 channels in Kiss1ARH neurons were deleted using CRISPR, the slow excitatory postsynaptic potential (sEPSP) was eliminated. Our data enabled us to formulate a biophysically realistic mathematical model of the Kiss1ARH neuron, suggesting that E2 modifies ionic conductances in Kiss1ARH neurons, enabling the transition from high frequency synchronous firing through NKB-driven activation of TRPC5 channels to a short bursting mode facilitating glutamate release. In a low E2 milieu, synchronous firing of Kiss1ARH neurons drives pulsatile release of GnRH, while the transition to burst firing with high, preovulatory levels of E2 would facilitate the GnRH surge through its glutamatergic synaptic connection to preoptic Kiss1 neurons.

neuroscience↗

bioRxiv2024

POMC neurons control fertility through differential signaling of MC4R in Kisspeptin neurons in the female mouse

Inactivating mutations in the melanocortin 4 receptor (MC4R) gene cause monogenic obesity. Interestingly, female patients also display various degrees of reproductive disorders, in line with the subfertile phenotype of MC4RKO female mice. However, the cellular mechanisms by which MC4R regulates reproduction are unknown. Kiss1 neurons directly stimulate gonadotropin-releasing hormone (GnRH) release through two distinct populations; the Kiss1ARH neurons, controlling GnRH pulses, and the sexually dimorphic Kiss1AVPV/PeN neurons controlling the preovulatory LH surge. Here, we show that Mc4r expressed in Kiss1 neurons regulates fertility in females. In vivo, deletion of Mc4r from Kiss1 neurons in female mice replicates the reproductive impairments of MC4RKO mice without inducing obesity. Conversely, reinsertion of Mc4r in Kiss1 neurons of MC4R null mice restores estrous cyclicity and LH pulsatility without reducing their obese phenotype. In vitro, we dissect the specific action of MC4R on Kiss1ARH vs Kiss1AVPV/PeN neurons and show that MC4R activation excites Kiss1ARH neurons through direct synaptic actions. In contrast, Kiss1AVPV/PeN neurons are normally inhibited by MC4R activation except under elevated estradiol levels, thus facilitating the activation of Kiss1AVPV/PeN neurons to induce the LH surge driving ovulation in females. Our findings demonstrate that POMCARH neurons acting through MC4R, directly regulate reproductive function in females by stimulating the "pulse generator" activity of Kiss1ARH neurons and restricting the activation of Kiss1AVPV/PeN neurons to the time of the estradiol-dependent LH surge, and thus unveil a novel pathway of the metabolic regulation of fertility by the melanocortin system.

neuroscience↗

bioRxiv2023

Structure-conditioned masked language models for protein sequence design generalize beyond the native sequence space

Machine learning has revolutionized computational protein design, enabling significant progress in protein backbone generation and sequence design. Here, we introduce Frame2seq, a structure-conditioned masked language model for protein sequence design. Frame2seq generates sequences in a single pass, achieves 49.1% sequence recovery on the CATH 4.2 test dataset, and accurately estimates the error in its own predictions, outperforming the autoregressive ProteinMPNN model with over six times faster inference. To probe the ability of Frame2seq to generate novel designs beyond the native-like sequence space it was trained on, we experimentally test 26 Frame2seq designs for de novo backbones with low identity to the starting sequences. We show that Frame2seq successfully designs soluble (22/26), monomeric, folded, and stable proteins (17/26), including a design with 0% sequence identity to native. The speed and accuracy of Frame2seq will accelerate exploration of novel sequence space across diverse design tasks, including challenging applications such as multi-objective optimization.

bioengineering↗

bioRxiv2022

Hypomorphism of a novel long ERα isoform causes severe reproductive dysfunctions in female mice

Estrogen receptor alpha (ER)-mediated estrogen signaling play a pivotal role in both reproductive and non-reproductive functions. Transcriptional regulation of ER gene is highly complex, with multiple transcript variants being differentially produced across the tissues. However, tissue-specific variation and physiological specificity of the ER variants are not yet fully understood. In an attempt to generate a Cre-dependently restorable ER-null mice for functional investigation of the genetic sufficiency, we unexpectedly produced ER hypomorphic mice with biased downregulation of a previously unappreciated long ER isoform that is enriched in the female reproductive organs (uterus and ovaries) and the pituitary but minimally expressed in the brain. Female homozygous mutant mice were capable of pregnancy but displayed irregular estrus cycle and rarely maintained alive newborns without significant morphological and pathological changes in reproductive system and the disruption of body weight homeostasis, indicating the vital role of this long isoform in female reproductive function. Collectively, our results define a tissue-specifically enriched long ER isoform and its preferential role in female reproductive function over body weight homeostasis.

physiology↗

bioRxiv2020

Insulin potentiates the synchronous firing of arcuate nucleus Kiss1 neurons that protects against diet-induced obesity

Kisspeptin (Kiss1) neurons are essential for reproduction, but their role in the control of energy balance and other homeostatic functions remains unclear. High frequency firing of hypothalamic arcuate Kiss1 (Kiss1ARH) neurons releases kisspeptin into the median eminence, and neurokinin B (NKB) and dynorphin onto neighboring Kiss1ARH neurons to generate a slow excitatory postsynaptic potential (EPSP) mediated by TRPC5 channels that entrains intermittent, synchronous firing of Kiss1ARH neurons. High frequency optogenetic stimulation of Kiss1ARH neurons releases glutamate to excite the anorexigenic proopiomelanocortin (POMC) neurons and inhibit the orexigenic neuropeptide Y/agouti-related peptide (AgRP) neurons via metabotropic glutamate receptors. At the molecular level, the endoplasmic reticulum calcium-sensing protein stromal interaction molecule 1 (STIM1) is critically involved in the regulation of neuronal Ca2+ signaling and neuronal excitability through its interaction with plasma membrane calcium (e.g., TRPC) channels. 17{beta}-estradiol (E2) downregulates Stim1 mRNA expression in female arcuate neurons. Therefore, we hypothesized that deletion of Stim1 in Kiss1ARH neurons would increase neuronal excitability and their synchronous firing, which ultimately would affect energy homeostasis. Using optogenetics in combination with whole-cell recording and GCaMP6 imaging in slices, we discovered that the deletion of Stim1 in Kiss1 neurons significantly increased the amplitude of the slow EPSP and augmented synchronous [Ca2+]i oscillations in Kiss1ARH neurons. Deletion of Stim1 in Kiss1ARH neurons amplified the actions of NKB and protected ovariectomized female mice from developing obesity and glucose intolerance with high-fat dieting. Therefore, STIM1 appears to play a critical role in regulating synchronous firing of Kiss1ARH neurons, which ultimately affects energy homeostasis. Significance StatementHypothalamic arcuate kisspeptin (Kiss1ARH) neurons are essential for stimulating the pulsatile release of gonadotropin releasing hormone (GnRH) and maintaining fertility. However, Kiss1ARH neurons appear to be a key player in coordinating energy balance with reproduction. The regulation of calcium channels and hence calcium signaling is critically dependent on the endoplasmic reticulum calcium-sensing protein stromal interaction molecule 1 (STIM1), which interacts with the plasma membrane calcium channels. We have conditionally deleted Stim1 in Kiss1ARH neurons and found that it significantly increased the excitability of Kiss1ARH neurons and protected ovariectomized female mice from developing obesity and glucose intolerance with high-fat dieting.

neuroscience↗

bioRxiv2020

Epigenetic reprogramming of plasmacytoid dendritic cells drives type I interferon-dependent differentiation of acute myeloid leukemias for therapeutic benefit

Pharmacological inhibition of epigenetic enzymes can have therapeutic benefit, particularly against hematological malignancies. While these agents can affect tumor cell growth and proliferation, recent studies have demonstrated that pharmacological de-regulation of epigenetic modifiers may additionally mediate anti-tumor immune responses. Here we discovered a novel mechanism of immune regulation through the inhibition of histone deacetylases (HDACs). In a genetically engineered model of t(8;21) AML, leukemia cell differentiation and therapeutic benefit mediated by the HDAC inhibitor panobinostat required activation of the type I interferon (IFN) signaling pathway. Plasmacytoid dendritic cells (pDCs) were identified as the cells producing type I IFN in response to panobinostat, through transcriptional activation of IFN genes concomitant with increased H3K27 acetylation at these loci. Depletion of pDCs abrogated panobinostat-mediated activation of type I IFN signaling in leukemia cells and impaired therapeutic efficacy, while combined treatment of panobinostat and recombinant IFN improved therapeutic outcomes. These discoveries offer a new therapeutic approach for t(8;21) AML and demonstrate that epigenetic rewiring of pDCs enhances anti-tumor immunity, opening the possibility of exploiting this cell type as a new target for immunotherapy.

cancer biology↗

bioRxiv2020

CRISPR Knockdown of Kcnq3 Attenuates the M-current in NPY/AgRP Neurons

Arcuate nucleus Neuropeptide Y/Agouti-related peptide (NPY/AgRP) neurons drive ingestive behavior in response to the internal and external environment of an organism. NPY/AgRP neurons are adjacent to the median eminence, a circumventricular organ, and circulating metabolic factors and hormones communicate the energy state of the animal via these neurons by altering the excitability of NPY/AgRP neurons, which produces an appropriate change in behavior to maintain homeostasis. One example of this plasticity is seen in the M-current, a subthreshold, non-inactivating K+ current that acts to modulate excitability. Fasting decreases while estradiol increases the M-current through regulation of subunit mRNA expression of Kcnq 2, 3, & 5. KCNQ2/3 heteromers are thought to mediate the majority of the M-current. Here we used a recently developed single adeno-associated viral (AAV) vector containing a recombinase-dependent Staphylococcus aureus Cas9 (SaCas9) and a single guide RNA against Kcnq3 to selectively delete Kcnq3 in NPY/AgRP neurons to produce a loss of function in the M-current. We found that this virus was effective at knocking down Kcnq3 but not Kcnq2 expression. With the reduced KCNQ3 channel expression NPY/AgRP neurons were more depolarized, exhibited a higher input resistance, and the rheobase current needed to induce firing was significantly reduced, indicative of increased excitability. Although the resulting decrease in the M-current did not overtly alter ingestive behavior, it did significantly reduce the locomotor activity as measured in open field testing. Therefore, the SaCas9-sgKcnq3 is efficient to knock down Kcnq3 expression thereby reducing the M-current and increasing the excitability of NPY/AgRP neurons.

neuroscience↗

bioRxiv2019

Space use and resource selection of bobcats in the Appalachian Mountains of western Virginia

Bobcats are an apex predator and a species of socio-cultural importance in the central Appalachian Mountains. Despite their importance, knowledge of bobcat spatial ecology in the region is sparse. We examined space use and resource selection of bobcats in the Appalachian Mountains of western Virginia during 3 biological seasons: breeding (January-March), kitten-rearing (April-September), and dispersal (October-December). We observed sex effects on all space use metrics, with male seasonal areas of use (SAU) approximately 3 times larger than female SAUs and male movement rates 1.5 times higher than females during all seasons. We found no seasonal effect on SAU size for either sex. Female movement rates increased during the kitten-rearing season, and male movement rates increased during the dispersal season. We examined seasonal bobcat resource selection at 2 hierarchical scales, selection of home ranges within the landscape (2nd order) and selection of locations within home ranges (3rd order). Female bobcats exhibited 2nd order selection for higher elevations and deciduous forest and avoidance of fields. Males exhibited 2nd order selection for higher elevations and fields. Male 2nd order selection appears to be driven largely by the spatial distribution of females, which is mediated through the valley and ridge topography of the study area. Sample size precluded 3rd order analysis for females, however males exhibited 3rd order selection for higher elevations, fields, and deciduous forest. Resource selection patterns varied seasonally for both sexes, possibly driven by seasonal shifts in prey availability. Our findings highlight the importance of forested ridges to bobcats in the region. Our findings also illustrate the differences in space use between sexes, which future research efforts should consider. Further research should investigate seasonal shifts in bobcat prey selection, which may further explain the seasonal resource selection shifts we observed, and highlight potential implications for prey species.

ecology↗