Biology subjects

Lee, H.

Publications and source records attributed to Lee, H..

At least 235 records · Page 13Linked to original sources

bioRxiv2023

Distinct effects of priming the brain using tDCS and observational practice: new evidence from brain effective connectivity.

Complex motor skills can be acquired while observing a model without physical practice. Transcranial direct-current stimulation (tDCS) applied to the primary motor cortex (M1) also facilitates motor learning. However, the effectiveness of observational practice for bimanual coordination skills is debated and there is little research on the effects of tDCS on acquiring bimanual skills and the underlying effective/causal brain connectivity. We compared the effect of primary motor cortex tDCS (M1-tDCS) to action-observation (AO) when acquiring a bimanual, two-ball juggling skill and characterized the brain causal connectivity patterns underlying each condition. Twenty healthy young adults with no juggling experience were randomly assigned to either video observation of a skilled juggler or anodal M1-tDCS. Thirty trials of juggling were performed and scored after the intervention. Resting-state EEG data were collected before and after the intervention. Information flow rate was applied to EEG source data to measure causal connectivity. Juggling scores were significantly higher in the AO group (p =.03). We found the strongest information exchange from (L) parietal to (R) parietal regions, strong bidirectional information exchange between (R) parietal and (R) occipital regions and an extensive network of activity that was (L) lateralized in the AO condition. In contrast, the M1-tDCS condition was characterized by bilateral long-range connections with the strongest information exchange from the (R) occipital region to the (R) temporal and (L) occipital regions. This study provides new results about the distinct network dynamics of priming the brain for skill acquisition using direct stimulation or indirect stimulation via action observation.

neuroscience↗

bioRxiv2023

Complex ecosystems lose stability when resource consumption is out of niche

Natural communities exhibit diverse dynamics, encompassing global stability, multi-stability, periodic oscillations, and chaotic fluctuations in species abundances. Resource-consumer interactions provide a lens for mechanistic understanding of community behaviors, yet only a globally stable equilibrium can exist in the original MacArthur resource-consumer model. Here we find that diverse dynamics emerges when species consume resources that contribute little to their own growth. Key to understanding these results is comparison of niche range (difference between growth-promoting resources of similar species) and consumption range (difference between growth-promoting resources and the resources that are actually consumed). If the consumption range is small, we observe global stability as in the MacArthur model. But when consumption range increases to about the niche range, stability is lost, giving rise to emergent alternative stable states, globally stable states but with species extinction, and slightly later, persistent fluctuations. Given its importance in dictating stability, we define the ratio between consumption and niche ranges as encroachment, and find that it predicts key community properties like diversity and attractor basins even after the instability transition. In particular, after the loss of stability (encroachment greater than one), species extinction increases approximately linearly with encroachment. Since encroachment relies only on intrinsic species properties, community stability is resilient to environmental changes such as resource supply and mortality rate. Encroachment provides a framework for capturing resource competition due to growth-consumption inconsistency in complex communities as well as a robust quantitative characterization of the resulting emergent dynamics.

ecology↗

bioRxiv2023

Alternative Polyadenylation Determines the Functional Landscape of Inverted Alu Repeats

Inverted Alu repeats (IRAlus) are abundantly found in the transcriptome, especially in introns and 3' UTRs. Yet, the biological significance of 3' UTR IRAlus remains largely unknown. Here, we find that IRAlus induce the silencing of genes involved in essential signaling pathways. We utilize J2 antibody to directly capture and map the double-stranded RNA structure of 3' UTR IRAlus in the transcriptome. Bioinformatic analysis reveals alternative polyadenylation as a major axis of IRAlus-mediated gene regulation. Notably, the expression of mouse double minute 2 (MDM2), an inhibitor of p53, is upregulated by the exclusion of IRAlus during UTR shortening, which is exploited to silence p53 during tumorigenesis. Moreover, the transcriptome-wide UTR lengthening in neural progenitor cells results in the global downregulation of genes associated with neurodegenerative diseases, such as amyotrophic lateral sclerosis, via IRAlus inclusion. Our study establishes the functional landscape of 3' UTR IRAlus and its role in human pathophysiology.

molecular biology↗

bioRxiv2023

Disruption of redox balance in glutaminolytic triple negative breast cancer by inhibition of glutamate export and glutaminase

In triple-negative breast cancer (TNBC) that relies on catabolism of amino acid glutamine, glutaminase (GLS) converts glutamine to glutamate, which facilitates glutathione synthesis by mediating the enrichment of intracellular cystine via xCT antiporter activity. To overcome chemo resistant TNBC, we have tested a strategy of disrupting cellular redox balance by inhibition of GLS and xCT by CB839 and Erastin, respectively. Key findings of our study include: 1. Dual metabolic inhibition (CB839+Erastin) led to significant increases of cellular superoxide level in both parent and chemo resistant TNBC cells, but superoxide level was distinctly lower in resistant cells. 2. Dual metabolic inhibition combined with doxorubicin or cisplatin induced significant apoptosis in TNBC cells and is associated with high degrees of GSH depletion. In vivo, dual metabolic inhibition plus cisplatin led to significant growth delay of chemo resistant human TNBC xenografts. 3. Ferroptosis is induced by doxorubicin (DOX) but not by cisplatin or paclitaxel. Addition of dual metabolic inhibition to DOX chemotherapy significantly enhanced ferroptotic cell death. 4. Significant changes in cellular metabolites concentration preceded transcriptome changes revealed by single cell RNA sequencing, underscoring the potential of capturing early changes in metabolites as pharmacodynamic markers of metabolic inhibitors. Here we demonstrated that 4-(3-[18F]fluoropropyl)-L-glutamic acid ([18F]FSPG) PET detected xCT blockade by Erastin or its analog in mice bearing human TNBC xenografts. In summary, our study provides compelling evidence for the therapeutic benefit and feasibility of non-invasive monitoring of dual metabolic blockade as a translational strategy to sensitize chemo resistant TNBC to cytotoxic chemotherapy.

cancer biology↗

bioRxiv2023

A mouse model of ZTTK syndrome reveals indispensable SON functions in organ development and hematopoiesis

Rare diseases are underrepresented in biomedical research, leading to insufficient awareness. Zhu-Tokita-Takenouchi-Kim (ZTTK) syndrome is a rare disease caused by genetic alterations that result in heterozygous loss-of-function of SON. While ZTTK syndrome patients suffer from numerous symptoms, the lack of model organisms hamper our understanding of both SON and this complex syndrome. Here, we developed Son haploinsufficiency (Son+/-) mice as a model of ZTTK syndrome and identified the indispensable roles of Son in organ development and hematopoiesis. Son+/- mice recapitulated clinical symptoms of ZTTK syndrome, including growth retardation, cognitive impairment, skeletal abnormalities, and kidney agenesis. Furthermore, we identified hematopoietic abnormalities in Son+/- mice, similar to those observed in human patients. Surface marker analyses and single-cell transcriptome profiling of hematopoietic stem and progenitor cells revealed that Son haploinsufficiency inclines cell fate toward the myeloid lineage but compromises lymphoid lineage development by reducing key genes required for lymphoid and B cell lineage specification. Additionally, Son haploinsufficiency causes inappropriate activation of erythroid genes and impaired erythroid maturation. These findings highlight the importance of the full gene dosage of Son in organ development and hematopoiesis. Our model serves as an invaluable research tool for this rare disease and related disorders associated with SON dysfunction.

genetics↗

bioRxiv2023

NaP-TRAP, a novel massively parallel reporter assay to quantify translation control.

The cis-regulatory elements encoded in a mRNA determine its stability and translational output. While there has been a considerable effort to understand the factors driving mRNA stability, the regulatory frameworks governing translational control remain elusive. We have developed a novel massively parallel reporter assay (MPRA) to measure mRNA translation, Nascent Peptide Translating Ribosome Affinity Purification (NaP-TRAP). NaP-TRAP measures translation in a frame specific manner through the immunocapture of epitope tagged nascent peptides of reporter mRNAs. In contrast to existing MPRA methods, NaP-TRAP does not require specialized equipment and is readily adaptable to steady-state and dynamic model systems. We have employed NaP-TRAP to quantify Kozak strength and the regulatory landscapes of 5 UTRs in the developing zebrafish embryo and in human cells, characterizing general and developmentally dynamic cis-regulatory elements. To this end, we identify U-rich motifs as general enhancers, and upstream ORFs and GC-rich motifs as global repressors of translation. We also observe a translational switch during the maternal-to-zygotic transition, where C-rich motifs shift from repressors to prominent activators of translation. Conversely, we show that microRNA sites in the 5 UTR repress translation following the zygotic expression of miR-430. Together these results demonstrate that NaP-TRAP is a versatile, accessible, and powerful method to decode the regulatory functions of UTRs across different systems.

molecular biology↗

bioRxiv2023

Pathological claustrum activity drives aberrant cognitive network processing in human chronic pain

Aberrant cognitive network activity and cognitive deficits are established features of chronic pain. However, the nature of cognitive network alterations associated with chronic pain and their underlying mechanisms require elucidation. Here, we report that the claustrum, a subcortical nucleus implicated in cognitive network modulation, is activated by acute painful stimulation and pain-predictive cues in healthy participants. Moreover, we discover pathological activity of the claustrum and a lateral aspect of the right dorsolateral prefrontal cortex (latDLPFC) in migraine patients. Dynamic causal modeling suggests a directional influence of the claustrum on activity in this latDLPFC region, and diffusion weighted imaging (DWI) verifies their structural connectivity. These findings advance understanding of claustrum function during acute pain and provide evidence of a possible circuit mechanism driving cognitive impairments in chronic pain.

neuroscience↗

bioRxiv2023

A natural cyclic peptide valinomycin enhances plant innate immunity

Various natural compounds as alternative agents for the chemical management of plant diseases have long been proposed. Valinomycin, a Streptomyces-derived cyclic peptide, acts as an antifungal agent against several plant pathogenic fungi, including Botrytis cinerea. Here, we report the novel function of valinomycin, plant immune-boosting. Valinomycin potentiates pattern-triggered immunity (PTI) and effector-triggered immunity (ETI) in Arabidopsis, leading to enhanced resistance against bacterial speck disease locally and systemically. Moreover, this plant immune-boosting activity of valinomycin is associated with plant hormonal signaling. Thus, we propose that valinomycin harbors potential as a biocontrol agent suppressing complex pathogen infections, such as bacteria and fungi.

plant biology↗

bioRxiv2023

Interfacial morphodynamics of proliferating microbial communities

In microbial communities, various cell types often coexist by occupying distinct spatial domains. What determines the shape of the interface between such domains--which in turn influences the interactions between cells and overall community function? Here, we address this question by developing a continuum model of a 2D spatially-structured microbial community with two distinct cell types. We find that, depending on the balance of the different cell proliferation rates and substrate friction coefficients, the interface between domains is either stable and smooth, or unstable and develops finger-like protrusions. We establish quantitative principles describing when these different interfacial behaviors arise, and find good agreement both with the results of previous experimental reports as well as new experiments performed here. Our work thus helps to provide a biophysical basis for understanding the interfacial morphodynamics of proliferating microbial communities, as well as a broader range of proliferating active systems.

biophysics↗

bioRxiv2023

Quantification of the escape from X chromosome inactivation with the million cell-scale human single-cell omics datasets reveals heterogeneity of escape across cell types and tissues

One of the two X chromosomes of females is silenced through X chromosome inactivation (XCI) to compensate for the difference in the dosage between sexes. Among the X-linked genes, several genes escape from XCI, which could contribute to the differential gene expression between the sexes. However, the differences in the escape across cell types and tissues are still poorly characterized because no methods could directly evaluate the escape under a physiological condition at the cell-cluster resolution with versatile technology. Here, we developed a method, single-cell Level inactivated X chromosome mapping (scLinaX), which directly quantifies relative gene expression from the inactivated X chromosome with droplet-based single-cell RNA-sequencing (scRNA-seq) data. The scLinaX and differentially expressed genes analyses with the scRNA-seq datasets of [~]1,000,000 blood cells consistently identified the relatively strong degree of escape in lymphocytes compared to myeloid cells. An extension of scLinaX for multi-modal datasets, scLinaX-multi, suggested a stronger degree of escape in lymphocytes than myeloid cells at the chromatin-accessibility level with a 10X multiome dataset. The scLinaX analysis with the human multiple-organ scRNA-seq datasets also identified the relatively strong degree of escape from XCI in lymphoid tissues and lymphocytes. Finally, effect size comparisons of genome-wide association studies between sexes identified the larger effect sizes of the PRKX gene locus-lymphocyte counts association in females than males. This could suggest evidence of the underlying impact of escape on the genotype-phenotype association in humans. Overall, scLinaX and the quantified catalog of escape identified the heterogeneity of escape across cell types and tissues and would contribute to expanding the current understanding of the XCI, escape, and sex differences in gene regulation.

genomics↗

bioRxiv2023

Development of covalent chemogenetic K2P channel activators

K2P potassium channels regulate excitability by affecting cellular resting membrane potential in the brain, cardiovascular system, immune cells, and sensory organs. Despite their important roles in anesthesia, arrhythmia, pain, hypertension, sleep, and migraine, the ability to control K2P function remains limited. Here, we describe a chemogenetic strategy termed CATKLAMP (Covalent Activation of TREK family K+ channels to cLAmp Membrane Potential) that leverages the discovery of a site in the K2P modulator pocket that reacts with electrophile-bearing derivatives of a TREK subfamily small molecule activator, ML335, to activate the channel irreversibly. We show that the CATKLAMP strategy can be used to probe fundamental aspects of K2P function, as a switch to silence neuronal firing, and is applicable to all TREK subfamily members. Together, our findings exemplify a new means to alter K2P channel activity that should facilitate studies both molecular and systems level studies of K2P function and enable the search for new K2P modulators.

biophysics↗

bioRxiv2023

KmerSV: a visualization and annotation tool for structural variants using Human Pangenome derived k-mers

SummaryKmerSV is a visualization and annotation tool for structural variants (SVs). It can be applied to assembly contigs or long-read sequences. Using k-mers it rapidly generates images and provides genome features of SVs. As an important feature, it utilizes the new Human Pangenome reference which provide haploid specific assemblies, addresses limitations in prior references and improves the discovery of SVs. Availability and implementationKmerSV is implemented in Python and available at github.com/sgtc-stanford/kmerSV

bioinformatics↗

bioRxiv2023

Open-source, high-throughput targeted in-situ transcriptomics for developmental biologists

Multiplexed spatial profiling of mRNAs has recently gained traction as a tool to explore the cellular diversity and the architecture of tissues. We propose a sensitive, open-source, simple and flexible method for the generation of in-situ expression maps of hundreds of genes. We exploit direct ligation of padlock probes on mRNAs, coupled with rolling circle amplification and hybridization-based in situ combinatorial barcoding, to achieve high detection efficiency, high throughput and large multiplexing. We validate the method across a number of species, and show its use in combination with orthogonal methods such as antibody staining, highlighting its potential value for developmental biology studies. Finally, we provide an end-to-end computational workflow that covers the steps of probe design, image processing, data extraction, cell segmentation, clustering and annotation of cell types. By enabling easier access to highthroughput spatially resolved transcriptomics, we hope to encourage a diversity of applications and the exploration of a wide range of biological questions.

molecular biology↗

bioRxiv2023

Exposure to aldehyde cherry e-liquid flavouring and its vape by-product disrupts pulmonary surfactant biophysical function

Over the last decade there has been a surge in vaping device usage, especially among adolescents, raising concerns for potentially related lung damage. Notoriously, there have been many e-cigarette or vaping-related lung injury (EVALI) cases resulting in hospitalisations and deaths. Although the vaping component vitamin E acetate has been linked to a large proportion of EVALI cases resulting in its widespread banning, one fifth of the cases remain unexplained. Furthermore, the overall long-term impact of vaping on respiratory health is poorly understood. A likely driver behind EVALI is pulmonary surfactant disruption, as it is the first point of contact for any inhaled toxicant in the alveoli, and abnormalities of its function are linked to some symptoms presented in EVALI cases. Aberrant biophysical function of the surfactant results in alveolar surface tension increase, causing alveolar collapse. Vaping chemicals with the potential to disrupt surfactant function must be hydrophobic molecules able to interact with surfactant components at the alveolar air-liquid interface. Recent findings have recorded the synthesis of highly hydrophobic acetal by-products of the base vaping chemical propylene glycol and common flavouring aldehydes, including the cherry flavouring benzaldehyde, not identified in preliminary e-liquid safety tests. This study provides evidence that benzaldehyde and its by-product, benzaldehyde propylene glycol acetal, have the potential to significantly disrupt surfactant biophysical function via interactions with surfactant proteins SP-B and/or SP-C, which may provide stable interactions within the surfactant film by forming associations with the sublayer of surfactant three-dimensional structure present at high lateral compression, i.e., expiration breathing. Data also suggest considerable vaping chemical loss to the experimental subphase, indicating potential further implications to the alveolar epithelial layer beneath.

pharmacology and toxicology↗

bioRxiv2023

Single cell decoding of drug induced transcriptomic reprogramming in triple negative breast cancers

BackgroundThe encoding of cell intrinsic resistance states in breast cancer reflects the contributions of genomic and non-genomic variation. However, identifying the potential contributions of each requires accurate measurement and subtraction of the contribution of clonal fitness from co-measurement of transcriptional states. Somatic genomic variation in gene dosage, copy number variation, is the dominant mutational mechanism in breast cancer contributing to transcriptional variation and has recently been shown to contribute to platinum chemotherapy resistance states. Here we deploy time series measurements of triple negative breast cancer single cell transcriptomes in conjunction with co-measured single cell copy number associated clonal fitness to identify the contributions of genomic and non-genomic mechanisms to drug associated transcription states. ResultsWe generated serial scRNA-seq data (126,556 cells) from triple negative breast cancer (TNBC) patient-derived xenograft (PDX) experiments over 2.5 years in duration, and matched it against genomic copy number single cell data from the same biological samples. We show that the cell memory of transcriptional states of TNBC tumors serially exposed to platinum identifies distinct clonal responses within individual tumours. Copy-number clones with high drug fitness leading to clonal sweeps exhibit less transcriptional reversion, whereas clones with weak drug fitness exhibit highly dynamic transcription on drug withdrawal. Pathway analysis shows that copy number associated and copy number independent transcripts converge on epithelial-mesenchymal transition (EMT) and cytokine signaling states associated with resistance. We show from trajectory analysis that transcriptional reversion exhibits hysteresis, indicating that new intermediate transcriptional states are generated by platinum exposure. ConclusionsWe discovered that copy number clones with strong genotype associated fitness under platinum became fixed in their states, resulting in minimal transcriptional reversion on drug withdrawal. In contrast clones with weaker fitness undergo non-genomic transcriptional plasticity and these distinct responses co-exist within single tumours. Together the data suggest that copy number associated and copy number independent transcriptional states may contribute to platinum drug resistance within individual tumours. The dominance of genomic or non-genomic mechanisms within individual polyclonal tumours has implications for approaches to restoration of drug sensitivity and re-treatment strategies. Data availabilityUploaded Data URL: https://ega-archive.org/studies/EGAS00001007242 Github manuscript: https://github.com/molonc/drug_resistant_material/

genomics↗

bioRxiv2023

A hematopoietic stem cell subset that retains memory of prior inflammatory stress accumulates in aging and clonal hematopoiesis

Inflammation activates many blood cell types, driving aging and malignancy. Yet, hematopoietic stem cells (HSCs) survive a lifetime of infection to sustain life-long blood production. To understand HSC adaptation to inflammation, we developed xenograft inflammation-recovery models and performed single cell multiomics on isolated human HSC. Two transcriptionally and epigenetically distinct HSC subsets expressing canonical HSC programs were identified. Only one showed sustained transcriptional and epigenetic changes after recovery from inflammatory treatments. This HSC inflammatory memory (HSC-iM) program is enriched in memory T cells and HSCs from recovered COVID-19 patients. Importantly, HSC-iM accumulates with age and with clonal hematopoiesis. Overall, heritable molecular alterations in a subset of human HSCs, an adaptation to long-term inflammatory stress, may predispose to heightened age-related risk of blood cancer and infection. One-Sentence SummaryInflammation across a lifetime rewires human HSCs to produce a distinct HSC subset with both beneficial and deleterious fitness consequences.

cell biology↗

bioRxiv2023

Genetic Variants That Modify the Neuroendocrine Regulation of Foraging Behavior in C. elegans

The molecular mechanisms underlying diversity in animal behavior are not well understood. A major experimental challenge is determining the contribution of genetic variants that affect neuronal gene expression to differences in behavioral traits. The neuroendocrine TGF-beta ligand, DAF-7, regulates diverse behavioral responses of Caenorhabditis elegans to bacterial food and pathogens. The dynamic neuron-specific expression of daf-7 is modulated by environmental and endogenous bacteria-derived cues. Here, we investigated natural variation in the expression of daf-7 from the ASJ pair of chemosensory neurons and identified common variants in gap-2, encoding a GTPase-Activating Protein homologous to mammalian SynGAP proteins, which modify daf-7 expression cell-non-autonomously and promote exploratory foraging behavior in a DAF-7-dependent manner. Our data connect natural variation in neuron-specific gene expression to differences in behavior and suggest that genetic variation in neuroendocrine signaling pathways mediating host-microbe interactions may give rise to diversity in animal behavior.

neuroscience↗

bioRxiv2023

Sulfasalazine promotes myogenic differentiation via increasing of fast myosin heavy chain isoforms

Sarcopenia is a debilitating condition characterized by the progressive and generalized degeneration of skeletal muscle mass and function. As of now, there is no approved pharmacological treatment for sarcopenia. Previously, our research revealed that Yin Yang 1 (YY1) plays a crucial role in PHD finger protein 20 (PHF20)-mediated myogenic differentiation. A significant enhancement in YY1 transcription, mediated by PHF20, was observed in C2C12 myoblasts. Within skeletal muscle, YY1 is traditionally considered to inhibit myogenesis by directly repressing the synthesis of late-stage differentiation genes, such as skeletal muscle actin, muscle creatine kinase, and myosin heavy chain IIb. Through screening of a drug library using a PHF20/YY1 promoter reporter assay, sulfasalazine emerged as a promising candidate. Sulfasalazine is known for its anti-inflammatory and immunomodulatory properties and is commonly prescribed for autoimmune diseases. In this study, the treatment of C2C12 myoblasts with sulfasalazine accelerated the myogenic differentiation and bolstered the gene and protein expression of fast myosin heavy chain via a metabolic shift towards glycolysis. Additionally, oral administration of sulfasalazine demonstrated improvement in physical performance in aged mice, as well as in mice models with hindlimb disuse or damage. Moreover, sulfasalazine exhibited a remarkable ability to facilitate the recovery of muscle fibers damaged by Velcro immobilization. Collectively, our findings suggest that sulfasalazine could represent a novel therapeutic avenue for the amelioration of muscle weakness, including sarcopenia.

biochemistry↗