Biology subjects

Kim, T.

Publications and source records attributed to Kim, T..

At least 91 records · Page 5Linked to original sources

bioRxiv2023

Combinatorial CRISPR screen reveals FYN and KDM4 as targets for synergistic drug combination for treating triple negative breast cancer

Tyrosine kinases play a crucial role in cell proliferation and survival and are extensively investigated as targets for cancer treatment. However, the efficacy of most tyrosine kinase inhibitors (TKIs) in cancer therapy is limited due to resistance. In this study, we identify a synergistic combination therapy involving TKIs for the treatment of triple negative breast cancer. By employing pairwise tyrosine kinase knockout CRISPR screens, we identify FYN and KDM4 as critical targets whose inhibition enhances the effectiveness of TKIs, such as NVP-ADW742 (IGF-1R inhibitor), gefitinib (EGFR inhibitor), and imatinib (ABL inhibitor) both in vitro and in vivo. Mechanistically, treatment with TKIs upregulates the transcription of KDM4, which in turn demethylates H3K9me3 at FYN enhancer for FYN transcription. This compensatory activation of FYN and KDM4 contributes to the resistance against TKIs. FYN expression is associated with therapy resistance and persistence by demonstrating its upregulation in various experimental models of drug-tolerant persisters and residual disease following targeted therapy, chemotherapy, and radiotherapy. Collectively, our study provides novel targets and mechanistic insights that can guide the development of effective combinatorial targeted therapies, thus maximizing the therapeutic benefits of TKIs.

cancer biology↗

bioRxiv2023

Phage-mediated resolution of genetic conflict alters the evolutionary trajectory of Pseudomonas aeruginosa lysogens

The opportunistic human pathogen Pseudomonas aeruginosa is naturally infected by a large class of temperate, transposable, Mu-like phages. We examined the genotypic and phenotypic diversity of P. aeruginosa PA14 populations as they resolve CRISPR autoimmunity, mediated by an imperfect CRISPR match to the Mu-like DMS3 prophage, and show that lysogen evolution is profoundly impacted by CRISPR autoimmunity and phage transposition around the chromosome. After 12 days of evolution, we measured a decrease in spontaneous induction in both exponential and stationary phase growth. Co-existing variation in spontaneous induction rates in exponential phase corresponded to a difference in the type of CRISPR self-targeting resolution, mediated either by host mutation or phage transposition. Multiple mutational modes to resolve genetic conflict between host and phage resulted in coexistence in evolved populations of single lysogens that maintained CRISPR immunity to other phages and polylysogens that have lost immunity completely. This work highlights a new dimension of the role of lysogenic phages in the evolution of their hosts. ImportanceThe chronic opportunistic multi-drug resistant pathogen Pseudomonas aeruginosa is persistently infected by temperate phages. We assess the contribution of temperate phage infection to the evolution of the clinically relevant strain UCBPP-PA14. We found that a low level of CRISPR-mediated self-targeting resulted in polylysogeny evolution and large genome rearrangements in lysogens; we also found extensive diversification in CRISPR spacers and cas genes. These genomic modifications resulted in decreased spontaneous induction in both exponential and stationary phase growth, increasing lysogen fitness. This work shows the importance of considering latent phage infection in characterizing the evolution of bacterial populations.

microbiology↗

bioRxiv2023

Neural correlates of crowding in macaque area V4

Visual crowding refers to the phenomenon where a target object that is easily identifiable in isolation becomes difficult to recognize when surrounded by other stimuli (distractors). Extensive psychophysical studies support two alternative possibilities for the underlying mechanisms. One hypothesis suggests that crowding results from the loss of visual information due to pooled encoding of multiple nearby stimuli in the mid-level processing stages along the ventral visual pathway. Alternatively, crowding may arise from limited resolution in decoding object information during recognition and the encoded information may remain inaccessible unless it is salient. To rigorously test these alternatives, we studied the responses of single neurons in macaque area V4, an intermediate stage of the ventral, object-processing pathway, to parametrically designed crowded displays and their texture-statistics matched metameric counterparts. Our investigations reveal striking parallels between how crowding parameters, e.g., number, distance, and position of distractors, influence human psychophysical performance and V4 shape selectivity. Importantly, we found that enhancing the salience of a target stimulus could reverse crowding effects even in highly cluttered scenes and such reversals could be protracted reflecting a dynamical process. Overall, we conclude that a pooled encoding of nearby stimuli cannot explain the observed responses and we propose an alternative model where V4 neurons preferentially encode salient stimuli in crowded displays. Significance StatementPsychophysicists have long studied the phenomena of visual crowding, but the underlying neural mechanisms are unknown. Our results reveal striking correlations between the responses of neurons in mid-level visual cortical area V4 and psychophysical demonstrations, revealing that crowding is influenced not only by the number and spatial arrangement of distractors but also by the similarity of features between target and distractors, as well as among the distractors themselves. Overall, our studies provide strong evidence that the visual system uses strategies to preferentially encode salient features in a visual scene presumably to process visual information efficiently. When multiple nearby stimuli are equally salient, the phenomenon of crowding ensues.

neuroscience↗

bioRxiv2023

Healthy adults favor stable left/right hand choices over performance at an unconstrained reach-to-grasp task

Reach-to-grasp actions are fundamental to the daily activities of human life, but few methods exist to assess individuals reaching and grasping actions in unconstrained environments. The Block Building Task (BBT) provides an opportunity to directly observe and quantify these actions, including left/right hand choices. Here we sought to investigate the motor and non-motor causes of left/right hand choices, and optimize the design of the BBT, by manipulating motor and non-motor difficulty in the BBTs unconstrained reach-to-grasp task We hypothesized that greater motor and non-motor (e.g. cognitive/perceptual) difficulty would drive increased usage of the dominant hand. To test this hypothesis, we modulated block size (large vs. small) to influence motor difficulty, and model complexity (10 vs. 5 blocks per model) to influence non-motor difficulty, in healthy adults (n=57). We hypothesized that healthy adults with high non-dominant hand performance in a precision drawing task should be more likely to use their non-dominant hand in the BBT. Our data revealed that increased motor and non-motor difficulty led to lower task performance (slower speed), but participants only increased use of their dominant hand only under the most difficult combination of conditions: in other words, participants allowed their performance to degrade before changing hand choices, even though participants were instructed only to optimize performance. These results demonstrate that hand choices during reach-to grasp actions are more stable than motor performance in healthy right-handed adults, but tasks with multifaceted difficulties can drive individuals to rely more on their dominant hand. Statements and DeclarationsDr. Philip and Washington University in St. Louis have a licensing agreement with PlatformSTL to commercialize the iPad app used in this study.

neuroscience↗

bioRxiv2023

Intra-ocular Predation of Fluoroquinolone-Resistant Pseudomonas aeruginosa and Serratia marcescens by the Predatory Bacteria

Endogenous endophthalmitis caused by Gram-negative bacteria is an intra-ocular infection that can rapidly progress to irreversible loss of vision. While most endophthalmitis isolates are susceptible to antibiotic therapy, the emergence of resistant bacteria necessitates alternative approaches to combat intraocular bacterial proliferation. In this study the ability of predatory bacteria to limit intraocular growth of Pseudomonas aeruginosa, Serratia marcescens, and Staphylococcus aureus was evaluated in a New Zealand White rabbit endophthalmitis prevention model. Predatory bacteria Bdellovibrio bacteriovorus and Micavibrio aeruginosavorus were able to reduce proliferation of keratitis isolates of P. aeruginosa and S. marcescens. However, it was not able to significantly reduce S. aureus, which is not a productive prey for these predatory bacteria, suggesting that the inhibitory effect on P. aeruginosa requires active predation rather than an antimicrobial immune response. Similarly, UV-inactivated B. bacteriovorus were unable to prevent proliferation of P. aeruginosa. Together, these data suggest in vivo predation of Gram-negative bacteria within the intra-ocular environment.

microbiology↗

bioRxiv2023

High-throughput identification of functional regulatory SNPs in systemic lupus erythematosus

Genome-wide association studies implicate multiple loci in risk for systemic lupus erythematosus (SLE), but few contain exonic variants, rendering systematic identification of non-coding variants essential to decoding SLE genetics. We utilized SNP-seq and bioinformatic enrichment to interrogate 2180 single-nucleotide polymorphisms (SNPs) from 87 SLE risk loci for potential binding of transcription factors and related proteins from B cells. 52 SNPs that passed initial screening were tested by electrophoretic mobility shift and luciferase reporter assays. To validate the approach, we studied rs2297550 in detail, finding that the risk allele enhanced binding to the transcription factor Ikaros (IKZF1), thereby modulating expression of IKBKE. Correspondingly, primary cells from genotyped healthy donors bearing the risk allele expressed higher levels of the interferon / NF-{kappa}B regulator IKK{varepsilon}. Together, these findings define a set of likely functional non-coding lupus risk variants and identify a new regulatory pathway involving rs2297550, Ikaros, and IKK{varepsilon} implicated by human genetics in risk for SLE.

genetics↗

bioRxiv2023

Top-down attention shifts behavioral and neural event boundaries in narratives with overlapping event scripts

Understanding and remembering the complex experiences of everyday life relies critically on prior schematic knowledge about how events in our world unfold over time. How does the brain construct event representations from a library of schematic scripts, and how does activating a specific script impact the way that events are segmented in time? We developed a novel set of 16 audio narratives, each of which combines one of four location-relevant event scripts (restaurant, airport, grocery store, lecture hall) with one of four socially-relevant event scripts (breakup, proposal, business deal, meet cute), and presented them to participants in an fMRI study and a separate online study. Responses in angular gyrus, parahippocampal gyrus, and subregions of medial prefrontal cortex (mPFC) were driven by both location and social script information, showing that these regions can track schematic sequences from multiple domains. For some stories participants were primed to attend to one of the two scripts, by training them to listen for and remember specific script-relevant episodic details. Activating a location-related event script shifted the timing of subjective event boundaries to align with script-relevant changes in the narratives, and this behavioral shift was mirrored in the timing of neural responses, with mPFC event boundaries (identified using a Hidden Markov Model) aligning to location-relevant rather than socially-relevant boundaries when participants were location primed. Our findings demonstrate that neural event dynamics are actively modulated by top-down goals, and provide new insight into how narrative event representations are constructed through the activation of temporally-structured prior knowledge.

neuroscience↗

bioRxiv2023

M1 recruitment during interleaved practice is important for encoding, not just consolidation, of novel skill memory

Primary motor cortex (M1) plays a major role in motor memory acquisition and retention in humans, but its role in interleaved practice (as opposed to repetitive practice) remains unknown. We anticipated that the improved retention typically associated with interleaved practice depends on M1, and thus cathodal transcranial direct current (ctDCS) stimulation to M1 during training would disrupt this improved retention. The benefits of interleaved practice have been reported to occur from more effective consolidation, manifested as rapid skill memory stabilization followed by more long-term enhancement. While we observed the expected decline in retention performance following interleaved practice paired with ctDCS, this reduced retention resulted from more modest encoding of novel skill memory during acquisition rather than from disruption of offline consolidation processes. These data highlight the broad role played by motor cortex for both encoding and retention of novel skill memory.

neuroscience↗

bioRxiv2023

Genome assembly of Hibiscus sabdariffa L. provides insights into biosynthetic pathways of medicinal natural products

Hibiscus sabdariffa L. is a widely cultivated herbaceous plant with diverse applications in food, tea, fiber, and medicine. In this study, we present a high-quality genome assembly of H. sabdariffa using more than 33 Gbps of high-fidelity (HiFi) long-read sequencing data at 20X coverage. The primary assembly and haplotype-resolved genomes exhibit an N50 contig length of 26.25 Mbps, 11.96 Mbps, and 14.50 Mbps, with a coverage of 141.3%, 86.0%, and 88.6%, respectively. By aligning 26 Gbps of total RNA sequencing data (PE100) extracted from leaves, we predicted 154k, 79k, and 87k genes in the respective genome. The completeness of the genomes and predicted genes was confirmed by benchmarking universal single-copy orthologs analysis on a eudicots_odb10 database, with a 99.3% complete rate for the primary assembly. The high-quality genome resource allowed the construction of genetic networks for phenylpropanoid and flavonoid metabolism, thereby facilitating the identification of candidate genes involved in the biosynthesis of key intermediates for roselle-specific medicinal natural products. Comprehensive genomic and functional analysis opens avenues for further exploration and application of valuable natural products derived from H. sabdariffa.

genomics↗

bioRxiv2023

Scalable covariance-based connectivity inference for synchronous neuronal networks

We present a novel method for inferring connectivity from large-scale neuronal networks with synchronous activity. Our approach leverages Dynamic Differential Covariance to address the associated computational challenges. First, we analyze spike trains generated from Leaky Integrate-and-Fire network simulations and evaluate the performance of several off-the-shelf multivariate connectivity inference methods. Next, we introduce a new approach, Fractional Dynamic Differential Covariance (FDDC), and demonstrate that it consistently outperforms the other methods. Finally, we apply FDDC to experimental data to assess the topological organization of inferred graphs of in vitro neural network recordings obtained using high-density microelectrode arrays (HD-MEAs). Our results indicate that FDDC-derived graphs exhibit a significant negative correlation between small-worldness and measures of network synchrony. In contrast, graphs inferred through the well-established pairwise correlation method do not show such a correlation. This finding implies that the graphs obtained through FDDC provide stronger evidence in support of the theoretical notion that networks with clustered connections tend to exhibit higher levels of synchronizability. We hypothesize that our findings have implications for the development of scalable connectivity inference methods for large-scale neural network data.

neuroscience↗

bioRxiv2023

STimage:robust, confident and interpretable models for predicting gene markers from cancer histopathological images

Spatial transcriptomic (ST) imaging and sequencing data enable us to link tissue morphological features with thousands of previously unseen gene expression values, opening a new horizon for understanding tissue biology and achieving breakthroughs in digital pathology. Deep learning models are emerging to predict gene expression or classify cell types using images as the sole input. Such models hold significant potential for clinical applications, but require improvements in interpretability and robustness. We developed STimage as a comprehensive suite of models for both regression (predicting gene expression) and classification (mapping tissue regions and cell types) tasks. STimage is the first to thoroughly address robustness (uncertainty) and interpretability. For robustness, STimage predicts gene expression based on parameter distributions rather than fixed data points, allowing for generalisation at a population scale. STimage estimates uncertainty from the data (aleatoric) and from the model (epistemic) for each of thousands of imaging tiles. STimage achieves interpretability by analysing model attribution at a single-cell level, and in the context of histopathological annotation. While existing models focus on predicting highly variable genes, STimage predicts functional genes and identifies highly predictable genes. Using diverse datasets from three cancers and one chronic disease, we assessed the models performance on in-distribution and out-of-distribution samples. STimage is robust to technical variations across platforms, data types, sample preservation methods, and disease types. Further, we implemented an ensemble approach, incorporating pre-trained foundation models, to improve performance and reliability, especially in cases with small training datasets. With single-cell resolution Xenium data, STimage could classify cell types for millions of individual cells. Applying STimage to proteomics data such as CODEX, we found that STimage can predict gene expression consistent with protein expression patterns. Finally, we showed that using STimage-predicted values based solely on imaging input, we could stratify patient survival groups. Overall, STimage advances spatial transcriptomics by improving the prediction of gene expression from traditional histopathological images, making it more accessible for tissue biology research and digital pathology applications.

bioinformatics↗

bioRxiv2023

Selenium reduction of ubiquinone via SQOR suppresses ferroptosis

The canonical biological function of selenium is in the production of selenocysteine residues of selenoproteins, and this forms the basis for its role as an essential antioxidant and cytoprotective micronutrient. Here, we demonstrate that selenium, via its metabolic intermediate hydrogen selenide, efficiently donates its electrons to ubiquinone to form ubiquinol in the mitochondria through catalysis by sulfide quinone oxidoreductase (SQOR). Hydrogen selenide is superior to hydrogen sulfide as an electron donor owing to its larger valence shell. We show that this mechanism, independently of selenoprotein production, protects against ferroptosis via ubiquinol production in a manner that depends on xCT mediated selenide formation and SQOR activity. Our findings identify a regulatory mechanism against ferroptosis that implicates SQOR and expands our understanding of selenium in biology.

biochemistry↗

bioRxiv2023

READRetro: Natural Product Biosynthesis Planning with Retrieval-Augmented Dual-View Retrosynthesis

Elucidating the biosynthetic pathways of natural products has been a major focus of biochemistry and pharmacy. However, predicting the whole pathways from target molecules to metabolic building blocks remains a challenge. Here we propose READRetro as a practical bio-retrosynthesis tool for planning the biosynthetic pathways of natural products. READRetro effectively resolves the tradeoff between generalizability and memorability in bio-retrosynthesis by implementing two separate modules; each module is responsible for either generalizability or memorability. Specifically, READRetro utilizes a rule-based retriever for memorability and an ensemble of two dual-representation-based deep learning models for generalizability. Through extensive experiments, READRetro was demonstrated to outperform existing models by a large margin in terms of both generalizability and memorability. READRetro was also capable of predicting the known pathways of complex plant secondary metabolites such as monoterpene indole alkaloids, demonstrating its applicability in the real-world bio-retrosynthesis planning of natural products. A website (https://readretro.net) and open-source code have been provided for READRetro, a practical tool with state-of-the-art performance for natural product biosynthesis research.

bioinformatics↗

bioRxiv2023

Predatory Bacteria can Reduce Pseudomonas aeruginosa Induced Corneal Perforation and Proliferation in a Rabbit Keratitis Model

PurposePseudomonas aeruginosa keratitis is a severe ocular infection that can lead to perforation of the cornea. In this study we evaluated the role of bacterial quorum sensing in generating corneal perforation and bacterial proliferation and tested whether co-injection of the predatory bacteria Bdellovibrio bacteriovorus could alter the clinical outcome. P. aeruginosa with lasR mutations were observed among keratitis isolates from a study collecting samples from India, so an isogenic lasR mutant strain of P. aeruginosa was included. MethodsRabbit corneas were intracorneally infected with P. aeruginosa strain PA14 or an isogenic {Delta}lasR mutant and co-injected with PBS or B. bacteriovorus. After 24 h, eyes were evaluated for clinical signs of infection. Samples were analyzed by scanning electron microscopy, optical coherence tomography, sectioned for histology, and corneas were homogenized for CFU enumeration and for inflammatory cytokines. ResultsWe observed that 54% of corneas infected by wild-type PA14 presented with a corneal perforation (n=24), whereas only 4% of PA14 infected corneas that were co-infected with B. bacteriovorus perforate (n=25). Wild-type P. aeruginosa proliferation was reduced 7-fold in the predatory bacteria treated eyes. The {Delta}lasR mutant was less able to proliferate compared to the wild-type, but was largely unaffected by B. bacteriovorus. ConclusionThese studies indicate a role for bacterial quorum sensing in the ability of P. aeruginosa to proliferate and cause perforation of the rabbit cornea. Additionally, this study suggests that predatory bacteria can reduce the virulence of P. aeruginosa in an ocular prophylaxis model.

microbiology↗

bioRxiv2023

Myomatrix arrays for high-definition muscle recording

Neurons coordinate their activity to produce an astonishing variety of motor behaviors. Our present understanding of motor control has grown rapidly thanks to new methods for recording and analyzing populations of many individual neurons over time. In contrast, current methods for recording the nervous systems actual motor output - the activation of muscle fibers by motor neurons - typically cannot detect the individual electrical events produced by muscle fibers during natural behaviors and scale poorly across species and muscle groups. Here we present a novel class of electrode devices ("Myomatrix arrays") that record muscle activity at unprecedented resolution across muscles and behaviors. High-density, flexible electrode arrays allow for stable recordings from the muscle fibers activated by a single motor neuron, called a "motor unit", during natural behaviors in many species, including mice, rats, primates, songbirds, frogs, and insects. This technology therefore allows the nervous systems motor output to be monitored in unprecedented detail during complex behaviors across species and muscle morphologies. We anticipate that this technology will allow rapid advances in understanding the neural control of behavior and in identifying pathologies of the motor system.

neuroscience↗

bioRxiv2023

Deep spatial-omics to aid personalization of precision medicine in metastatic recurrent Head & Neck Cancers

Immune checkpoint inhibitor (ICI) modality has had a limited success (<20%) in treating metastatic recurrent Head & Neck Oropharyngeal Squamous cell carcinomas (OPSCCs). To improve response rates to ICIs, tailored approaches capable to capture the tumor complexity and dynamics of each patients disease are needed. Here, we performed advanced analyses of spatial proteogenomic technologies to demonstrate that: (i) compared to standard histopathology, spatial transcriptomics better-identified tumor cells and could specifically classify them into two different metabolic states with therapeutic implications; (ii) our new method (Spatial Proteomics-informed cell deconvolution method or SPiD) improved profiling of local immune cell types relevant to disease progression, (iii) identified clinically relevant alternative treatments and a rational explanation for checkpoint inhibitor therapy failure through comparative analysis of pre- and post-failure tumor data and, (iv) discovered ligand-receptor interactions as potential lead targets for personalized drug treatments. Our work establishes a clear path for incorporating spatial-omics in clinical settings to facilitate treatment personalization.

cancer biology↗

bioRxiv2023

C3 in the 10-20 system may not be the best target for the motor hand area

The C3 region in the international 10-20 system for electroencephalography (EEG) recording is assumed to represent the right motor hand area. Therefore, in the absence of transcranial magnetic stimulation (TMS) or a neuronavigational system, neuromodulation methods, such as transcranial direct current stimulation, target C3 or C4, based on the international 10-20 system, to influence the cortical excitability of the right and left hand, respectively. The purpose of this study is to compare the peak-to-peak motor evoked potential (MEP) amplitudes of the right first dorsal interosseus (FDI) muscle after single-pulse TMS at C3, C3h, and C1. Using an intensity of 110% of the resting motor threshold, 15 individual MEPs from each of C3, C3h, C1, and hotspots were randomly recorded from FDI for sixteen right-handed undergraduate students. Average MEPs were greatest at C3h and C1, with both being larger than those recorded at C3. These data are congruent with recent findings using topographic analysis of individual MRIs that revealed poor correspondence between C3/C4 and the respective hand knob. Implications for the use of scalp locations determined using the 10-20 system for localizing the hand area are highlighted. HighlightsO_LIMEPs recorded at C3h and C1 were larger than those recorded at C3. C_LIO_LIScalp locations other than C3 offer a more accurate estimation of human hand area. C_LI

neuroscience↗

bioRxiv2023

A thin-film optogenetic visual prosthesis

Retinitis pigmentosa and macular degeneration lead to photoreceptor death and loss of visual perception. Despite recent progress, restorative technologies for photoreceptor degeneration remain largely unavailable. Here, we describe a novel optogenetic visual prosthesis (FlexLED) based on a combination of a thin-film retinal display and optogenetic activation of retinal ganglion cells (RGCs). The FlexLED implant is a 30 {micro}m thin, flexible, wireless {micro}LED display with 8,192 pixels, each with an emission area of 66 {micro}m2. The display is affixed to the retinal surface, and the electronics package is mounted under the conjunctiva in the form factor of a conventional glaucoma drainage implant. In a rabbit model of photoreceptor degeneration, optical stimulation of the retina using the FlexLED elicits activity in visual cortex. This technology is readily scalable to hundreds of thousands of pixels, providing a route towards an implantable optogenetic visual prosthesis capable of generating vision by stimulating RGCs at near-cellular resolution.

neuroscience↗