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Koehler, J.

Publications and source records attributed to Koehler, J..

13 recordsLinked to original sources

JAK inhibition overcomes first-line drug resistance in a pre-clinical model of epilepsy

One-third of people with epilepsy continue to have seizures despite antiseizure medications (ASMs), and available therapies often fail to improve disabling cognitive comorbidities. Patients with drug resistant epilepsy report that the adverse effects of medications along with their comorbidities can have a greater negative impact on the quality of life than seizures. We previously identified recurrent JAK/STAT3 activation in chronic epilepsy and showed that transient treatment with the JAK inhibitor tofacitinib (CP690550) durably suppresses seizures and restores cognition in mice. Here, we tested CP690550 as an add-on therapy after failure of carbamazepine (CBZ), a common first line treatment for epilepsy, in a mouse model of multifocal temporal lobe epilepsy. In CBZ-resistant animals, dual therapy with CP690550 reduced median seizure frequency and time spent seizing by an order of magnitude; most dual therapy responders had no observed behavioral seizures during treatment. CP690550 also restored spatial working and short-term memory. We found that cognitive rescue was independent of seizure response. Our work suggests that JAK/STAT inhibition can overcome ASM nonresponse while independently improving epilepsy-associated cognitive dysfunction.

neuroscience↗

H3K27me3 maintains baseline network excitability after status epilepticus

The processes by which epileptic insults precipitate the molecular, cellular, and network alterations in the brain that lead to epilepsy are poorly understood. We previously discovered that after status epilepticus (SE - an epilepsy inducing severe bout of seizures) the H3K27 methylase Enhancer of Zeste Homolog 2 (EZH2) is robustly induced and drives repression of genes. Both systemic pharmacological inhibition of EZH2 and deletion of EZH2 in neurons exacerbates epilepsy progression, suggesting that acute EZH2 induction may exert a net protective effect against disease progression chronically. However, the mechanisms underlying EZH2-mediated control of the putative protective and pathological pathways in disease progression are still unknown. To interrogate the mechanisms of EZH2 function post-SE, we used bulk CUT&RUN- sequencing against H3K27me3 in tandem with bulk RNA-sequencing in hippocampi of naive and 4d. post-SE mice to profile epigenomic and transcriptomic changes. Differential peak analysis showed that H3K27me3 was enriched both at loci pre-marked by H3K27me3 in the naive hippocampus as well as in loci that were de novo methylated after SE, consistent with the SE-dependent induction of EZH2 protein levels. Multi-omic integration of CUT&RUN and RNA-seq data revealed a module of genes that were coordinately H3K27me3 enriched, transcriptionally repressed, and annotated to ontological terms involved in neuronal signaling and network excitability. This result suggests that EZH2 induction may function in part to control network excitability after injury. To test this, we treated mice acutely post-SE with the EZH2 inhibitor UNC1999 and found that EZH2 inhibition attenuated H3K27me3 induction and dampened repression of target network excitability genes in response to SE. Functionally, UNC1999 treatment significantly increased seizure probability acutely and exacerbated disease severity in the chronic period. Taken together, these results suggest that EZH2 induction after injury may function to maintain network excitability to lower seizure probability acutely to protect against disease progression.

neuroscience↗

Blooms like it hot, but mussels do not: Influence of invasive quagga mussels on cyanobacteria during summer

Quagga mussels (Dreissena rostriformis bugensis) are among the most impactful invaders in freshwaters of the Northern Hemisphere. As filter-feeders, they can reduce harmful algal blooms (HABs), but their effects are expected to be dependent on cyanobacteria species and water temperature. However, conclusive studies on these traits and their combination are lacking. Here, we combined laboratory experiments with an analysis of long-term data from a temperate shallow lake 10 years before and after quagga mussel invasion, respectively. We tested the hypotheses that quagga mussel filtration rates in the laboratory would 1) vary among common cyanobacteria species and 2) decrease above a critical temperature. Regarding the field data, we expected that 3) quagga mussels can reduce the summer biovolume of palatable cyanobacteria, but that 4) this effect disappears above a critical temperature. Our results support all four hypotheses. In laboratory experiments, Dolichospermum flos-aquae was classified as palatable to quagga mussels, while Aphanizomenon flos-aquae, Anabaenopsis elenkinii and Microcystis aeruginosa were less-palatable cyanobacteria. Filtration rates decreased above 28.9{degrees}C (CI: 27.6-30.2{degrees}C) with mussels dying at 32{degrees}C. Our long-term lake data show that cyanobacteria biovolumes were lower after quagga mussel invasion, but only below 27.7{degrees}C (CI: 26.9-28.4{degrees}C), confirming a critical thermal window for quagga mussel filtration. Global warming will therefore facilitate HABs by increasing the growth rates of cyanobacteria and reducing the filtration rates of quagga mussels above critical summer water temperatures, which are increasingly being reached in invaded lakes. This critical thermal window must be considered when making HAB predictions. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=93 SRC="FIGDIR/small/707163v1_ufig1.gif" ALT="Figure 1"> View larger version (19K): org.highwire.dtl.DTLVardef@175851eorg.highwire.dtl.DTLVardef@76a481org.highwire.dtl.DTLVardef@12a3965org.highwire.dtl.DTLVardef@11e3e7d_HPS_FORMAT_FIGEXP M_FIG C_FIG

ecology↗

Motion sequencing reveals hidden patterns of repetitive behavior in a mouse model of epilepsy

Epilepsy is the 4th most prevalent neurological condition with 50 million cases worldwide. Patients with epilepsy bare a disproportionate burden of cognitive decline and psychiatric disorders which remain poorly understood and go unaddressed by current anti-epileptic treatments. Furthermore, pre-clinical work on behavioral comorbidities can be hampered by current testing frameworks which rely on well-defined, discreet tests with limited repeatability. Recent work has demonstrated a role for machine learning modalities such as Motion Sequencing (MoSeq) in assessing behavioral differences between naive and epileptic. In this study we combined MoSeq with a novel analysis pipeline to uncover repetitive behaviors in chronically epileptic mice. These repetitive behaviors emerge alongside epilepsy specific racing behaviors which persist in epileptic mice as disease progresses. We show that epileptic mice have more fragile and dispersed behavioral networks. Finally, we test this pipeline using the FDA approved anti-seizure medication carbamazepine, showing a rescue of racing syllable and a partial rescue of behavioral network dispersion. Together, these results lay a groundwork for extracting clinically relevant phenotypes from MoSeq data throughout disease progression.

neuroscience↗

ReaxFF-guided Optimisation of VIRIP-based HIV-1 Entry Inhibitors

Peptides hold great promise for safe and effective treatment of viral infections. However, their use is often constrained by limited efficacy and high production costs, especially for long or complex peptide chains. Here, we used ReaxFF molecular dynamics (MD) simulations to optimize the size and activity of VIRIP (Virus Inhibitory Peptide), a naturally occurring 20-residue fragment of 1-antitrypsin that binds the HIV-1 GP41 fusion peptide (FP), thereby blocking viral fusion and entry into host cells. Specifically, we used the NMR structure of the complex between an optimized VIRIP derivative (VIR-165) and the HIV-1 gp41 FP for ReaxFF-guided in silico analysis, evaluating the contribution of each amino acid in the interaction of the inhibitor with its viral target. This approach allowed us to reduce the size of the HIV-1 FP inhibitor from 20 to 10 amino acids (2.28 to 1.11 kDa). HIV-1 infection assays showed that the size-optimized VIRIP derivative (soVIRIP) retains its broad-spectrum anti-HIV-1 capability and is non-toxic in the vertebrate zebrafish model. Compared to the original VIRIP, soVIRIP displayed more than 100-fold higher antiviral activity (IC50 of [~]120 nM). Thus, it is more potent than a dimeric 20-residue VIRIP derivative (VIR-576) that was proven safe and effective in a phase I/II clinical trial. Our results show that ReaxFF-based MD simulations represent a suitable approach for the optimization of therapeutic peptides.

molecular biology↗

Minimally Invasive DNA-Mediated Photostabilization for Extended Single-Molecule and Super-resolution Imaging

Photobleaching of fluorescence labels poses a major limitation in single-molecule and super-resolution microscopy. Conventional photostabilization methods, such as oxygen removal and addition of high concentrations of photostabilization additives, often require careful fluorophore selection and can disrupt the biological environment. To address these limitations, we developed a modular and minimally invasive photostabilization approach that utilizes DNA-mediated delivery of a photostabilizer directly to the imaging site. Under lower excitation intensities, the DNA-mediated strategy outperformed solution-based approaches, achieving efficient photostabilization at significantly lower additive concentrations. However, at higher excitation intensities, the stability of a single photostabilizer molecule became the limiting factor. To overcome this and reduce the loss of localizations in DNA-PAINT experiments we have also implemented a recovery scheme where the photostabilizer is continuously replenished at the imaging site. We further extended the approach to cell imaging, demonstrating improved localization rate and precision in 3D-DNA PAINT measurements. DNA-mediated photostabilization offers a promising solution for imaging applications where high additive concentrations are prohibited. Its modularity enables adaptation to various imaging schemes and ultimately expands the repertoire of fluorophores suitable for single-molecule and super-resolution imaging.

biophysics↗

The selfish yet forgetful brain: Stable cerebral oxygen metabolism during hypoglycemia but impaired memory consolidation

The continuous supply of glucose and oxygen is essential for healthy brain function. Accordingly, the Selfish Brain Theory proposes that the human brain prioritizes its own energy demands, making it less vulnerable to fluctuations in systemic energy availability. Although studies have reported decreases in cerebral glucose metabolism, alternative energy sources other than glucose might be oxidized for ATP production. However, cerebral oxygen metabolism (CMRO2) has never been quantified across the human brain. In this study, we investigated the influence of insulin-induced hypoglycemia on CMRO2 in healthy male participants. Additionally, we explored the prolonged effects of hypoglycemia on cognitive function following the restoration of euglycemia. We found that CMRO2 remained stable under hypoglycemia, even at blood glucose levels below 49 mg/dL. Interestingly, we detected a significant increase in cerebral blood flow (CBF) of up to 11%, particularly in regions involved in higher cognitive processing. Despite stable rates of oxygen metabolism, we identified a selective impairment in memory consolidation following hypoglycemia, even after normal glucose levels were restored, with no effects observed in memory encoding or attention. In favor of the Selfish Brain Theory, the stability in CMRO2 suggests that the brain efficiently shifts to alternate energy pathways under hypoglycemia, potentially using astrocytic glycogen. Despite this metabolic flexibility, our results indicate that prior hypoglycemia imposes long-lasting effects on memory consolidation, possibly linked to glycogen depletion and impaired glutamate synthesis. In summary, our study suggests that clinical states of hypoglycemia pose a critical impact on patient brain health and functioning.

neuroscience↗

Machine Learning Driven Simulations of SARS-CoV-2 Fitness Landscape

Predicting protein variant effects is a key challenge in preparing for pathogenic viral strains, understanding mutation-linked diseases, and designing new proteins. Protein sequence-structure-function relationships are difficult to model due to complex allosteric and epistatic effects. To investigate efficient modeling strategies, we trained supervised machine learning (ML) models with deep mutational scanning (DMS) libraries of SARS-CoV-2 receptor binding domain (RBD) sequences labeled with angiotensin converting enzyme 2 (ACE2) binding affinity. These models demonstrate superior performance predicting combinatorial mutation effects compared to adding or averaging the effects of point mutations and exhibit strong extrapolative performance ranking omicron variants when training only on wild type (WT) variants. We characterize the RBD fitness landscape combining ML with Markov Chain Monte Carlo simulations to predict evolutionary patterns from the WT sequence, and generate comparable sequence profiles to high fitness sequences in DMS data predicting mutations in unseen omicron variants. These models provide insight into the relationship between RBD sequence elements, and offer a new perspective on the use of DMS to predict emerging viral strains, which we anticipate will be applicable to other evolutionary prediction tasks. To facilitate application and future development of this strategy, we introduce Mavenets: https://github.com/SztainLab/mavenets.

bioinformatics↗

Liver Fibroblast Growth Factor 21 (FGF21) is Required for the Full Anorectic Effect of the Glucagon-Like Peptide-1 Receptor Agonist Liraglutide in Male Mice fed High Carbohydrate Diets

Glucagon-like peptide-1 receptor (GLP-1R) agonists and fibroblast growth factor 21 (FGF21) confer similar metabolic benefits. Studies report that GLP-1RA induce FGF21. Here, we investigated the mechanisms engaged by the GLP-1R agonist liraglutide to increase FGF21 levels and the metabolic relevance of liraglutide-induced FGF21. We show that liraglutide increases FGF21 levels via neuronal GLP-1R activation. We also demonstrate that lack of liver Fgf21 expression confers partial resistance to liraglutide-induced weight loss. Since FGF21 reduces carbohydrate intake, we tested whether the contribution of FGF21 to liraglutide-induced weight loss is dependent on dietary carbohydrate content. In control and liver Fgf21 knockout (LivFgf21-/-) mice fed calorically matched diets with low- (LC) or high-carbohydrate (HC) content, we found that only HC-fed LivFgf21-/- mice were resistant to liraglutide-induced weight loss. Similarly, liraglutide-induced weight loss was partially impaired in LivFgf21-/- mice fed a high-fat, high-sugar (HFHS) diet. Lastly, we show that loss of neuronal {beta}-klotho expression also diminishes liraglutide-induced weight loss in mice fed a HC or HFHS diet, indicating that FGF21 mediates liraglutide-induced weight loss via neuronal FGF21 action. Our findings support a novel role for a GLP-1R-FGF21 axis in regulating body weight in the presence of high dietary carbohydrate content.

physiology↗

Vesicle-bound regulatory RNAs are associated with tissue aging

Previous work on murine models and human demonstrated global as well as tissue-specific molecular aging trajectories in solid tissues and body fluids1-8. Extracellular vesicles like exosomes play a crucial role in communication and information exchange in between such systemic factors and solid tissues9,10. We sequenced freely circulating and vesicle-bound small regulatory RNAs in mice at five time points across the average life span from 2 to 18 months. Intriguingly, each small RNA class exhibits unique aging patterns, which showed differential signatures between vesicle-bound and freely circulating molecules. In particular, tRNA fragments showed overall highest correlation with aging which also matched well between sample types, facilitating age prediction with non-negative matrix factorization (86% accuracy). Interestingly, rRNAs exhibited inverse correlation trajectories between vesicles and plasma while vesicle-bound microRNAs (miRNAs) were exceptionally strong associated with aging. Affected miRNAs regulate the inflammatory response and transcriptional processes, and adipose tissues show considerable effects in associated gene regulatory modules. Finally, nanoparticle tracking and electron microscopy suggest a shift from overall many small to fewer but larger vesicles in aged plasma, potentially contributing to systemic aging trajectories and affecting the molecular aging of organs.

molecular biology↗

PEA15 loss of function and defective cerebral development in the domestic cat

Cerebral cortical size and organization are critical features of neurodevelopment and human evolution, for which genetic investigation in model organisms can provide insight into developmental mechanisms and the causes of cerebral malformations. However, some abnormalities in cerebral cortical proliferation and folding are challenging to study in laboratory mice due to the absence of gyri and sulci in rodents. We report an autosomal recessive allele in domestic cats associated with impaired cerebral cortical expansion and folding, giving rise to a smooth, lissencephalic brain, and that appears to be caused by homozygosity for a frameshift in PEA15 (phosphoprotein expressed in astrocytes-15). Notably, previous studies of a Pea15 targeted mutation in mice did not reveal structural brain abnormalities. Affected cats, however, present with a non-progressive hypermetric gait and tremors, develop dissociative behavioral defects and aggression with age, and exhibit profound malformation of the cerebrum, with a 45% average decrease in overall brain weight, and reduction or absence of the ectosylvian, sylvian and anterior cingulate gyrus. Histologically, the cerebral cortical layers are disorganized, there is substantial loss of white matter in tracts such as the corona radiata and internal capsule, but the cerebellum is relatively spared. RNA-seq and immunohistochemical analysis reveal astrocytosis. Fibroblasts cultured from affected cats exhibit increased TNF-mediated apoptosis, and increased FGFb-induced proliferation, consistent with previous studies implicating PEA15 as an intracellular adapter protein, and suggesting an underlying pathophysiology in which increased death of neurons accompanied by increased proliferation of astrocytes gives rise to abnormal organization of neuronal layers and loss of white matter. Taken together, our work points to a new role for PEA15 in development of a complex cerebral cortex that is only apparent in gyrencephalic species. SummaryGyrification is the neurodevelopmental process in certain mammalian species during which the cerebral cortex expands and folds resulting in the classic wrinkled appearance of the brain. Abnormalities in this process underlie many congenital malformations of the brain. However, unlike many other human malformations, genetic insight into gyrification is not possible in laboratory mice because rodents have a lissencephalic or smooth cerebral cortex. We identified a mutation in domestic cats that likely causes failure of the cerebral cortex to expand and fold properly, and discovered that the mutation impairs production of a protein, PEA15 (phosphoprotein expressed in astrocytes-15), involved in intracellular signaling. Affected cats have profound abnormalities in brain development, with minimal changes in their superficial behavior and neurologic function. Additional studies of tissue and cultured cells from affected animals suggest a pathophysiologic mechanism in which increased death of neurons accompanied by increased cell division of astrocytes gives rise to abnormal organization of neuronal layers and loss of white matter. These results provide new insight into a developmental process that is unique to animals with gyrencephalic brains.

genetics↗

FDA-ARGOS: A Public Quality-Controlled Genome Database Resource for Infectious Disease Sequencing Diagnostics and Regulatory Science Research

Infectious disease next generation sequencing (ID-NGS) diagnostics are on the cusp of revolutionizing the clinical market. To facilitate this transition, FDA proactively invested in tools to support innovation of emerging technologies. FDA and collaborators established a publicly available database, FDA dAtabase for Regulatory-Grade micrObial Sequences (FDA-ARGOS), as a tool to fill reference database gaps with quality-controlled genomes. This manuscript discusses quality control metrics for the proposed FDA-ARGOS genomic resource and outlines the need for quality-controlled genome gap filling in the public domain. Here, we also present three case studies showcasing potential applications for FDA-ARGOS in infectious disease diagnostics, specifically: assay design, reference database and in silico sequence comparison in combination with representative microbial organism wet lab testing; a novel composite validation strategy for ID-NGS diagnostics. The use of FDA-ARGOS as an in silico comparator tool could reduce the burden for completing ID-NGS clinical trials. In addition, use cases identifying Enterococcus avium and Ebola virus (Zaire ebolavirus variant Makona) demonstrate the utility of FDA-ARGOS as a reference database for independent performance validation of new tests and for documenting how one would use this database as an in silico sequence target comparator tool for ID-NGS validation, respectively.

microbiology↗

Candida albicans dispersed cells signify a developmental state distinct from biofilm and planktonic phases

Candida albicans surface-attached biofilms are sites of amplification of an infection through continuous discharge of cells capable of initiating new infectious foci. Yeast cells released from biofilms on intravenous catheters have direct access to the bloodstream. We previously reported that dispersed cells are largely lateral yeast cells that originate from the hyphal layers of the biofilm. Compared to their planktonic counterparts, these biofilm-dispersed yeast cells displayed enhanced virulence-associated gene expression and drug resistance. Little is known about the molecular properties of dispersed cells. We found that the inducer of dispersal, PES1, genetically interacts with the repressor of filamentation, NRG1, in a manner that supports a genetic definition of dispersed cells as yeast. We combined a flow biofilm model with RNA sequencing technology, to identify transcriptomic characteristics of freshly dispersed yeast cells versus biofilms or age-matched planktonic yeast cells growing in glucose-rich medium. Dispersed cells largely inherited a biofilm-like mRNA profile but with one stark difference: dispersed cells were transcriptionally reprogrammed to metabolize alternative carbon sources, while their sessile parents expressed glycolytic genes, despite exposure to the same nutritional signals. Our studies hence define dispersal cell production as an intrinsic step of biofilm development which generates propagules capable of colonizing distant host sites. This developmental step anticipates the need for virulence-associated gene expression before experiencing the associated external signals.

microbiology↗