Biology subjects

Lee, R.

Publications and source records attributed to Lee, R..

At least 37 records · Page 2Linked to original sources

bioRxiv2025

Blocking somatic repeat expansion and lowering huntingtin via RNA interference synergize to prevent Huntingtons disease pathogenesis in mice

Huntingtons disease (HD) is a progressive neurodegenerative disorder with no approved therapies. Two major molecular drivers--somatic expansion of inherited CAG repeats and toxic mutant HTT (mHTT) variants--lead to neuronal dysfunction. Despite multiple trials, HTT-lowering strategies have not shown meaningful clinical benefit. Using therapeutic divalent siRNAs, we assessed the long-term impact of silencing MSH3 (a key regulator of somatic expansion), HTT, or both. In Q111 HD mice (>110 CAGs), which exhibit robust expansion, mHTT inclusions, and transcriptional dysregulation by 12 months, long-term MSH3 silencing blocked expansion, reduced inclusions, and reversed gene expression changes. HTT silencing alone had limited effect, but combined MSH3/HTT targeting synergistically eliminated inclusions and restored transcriptomic profiles. Parallel treatment in wild-type mice showed no toxicity, supporting the safety of long-term intervention. These findings position somatic expansion as a promising therapeutic target and demonstrate the potential of RNAi-based co-silencing of MSH3 and HTT as a disease-modifying strategy for HD.

neuroscience↗

bioRxiv2025

Multimodal profiling unveils a reversible basal-like breast cancer cell state resistant to AKT inhibition

The PI3K/AKT/mTOR pathway is central to cell metabolism and growth. However, pharmacological inhibition of the pathway is not uniformly effective across cancer types, or even within a single cancer model. In this study, we leverage oblique plane microscopy of triple negative breast cancer organoids, as well as lineage tracing to uncover a source of heterogeneity. Non-genetic resistance to AKT inhibition is associated with basal cell features of normal breast epithelium and the master transcription factor of basal cell state, {Delta}Np63, is sufficient to confer resistance. Cells can transition between states within four weeks and therefore, AKT inhibition only delays tumour growth, with tumours rich in KRT14+ cells resulting. Thus, under selection, triple negative breast cancer exploits a repertoire of cell states inherent to the breast.

cancer biology↗

bioRxiv2025

Enkephalinergic Neurons Gate Sex-Specific Control of Voluntary Micturition

Barringtons nucleus (Bar) is a brainstem hub essential for lower urinary tract (LUT) function, yet the molecular identity and functional specialization of its neuronal subtypes remain poorly defined. Here, we construct a single-nucleus transcriptional atlas of Bar and identify an excitatory Penk- expressing population (Bar-Penk) critical for LUT regulation. Bar-Penk neurons are selectively active during voiding, when the external urethral sphincter (EUS) relaxes, and their optogenetic activation elicits time-locked suppression of EUS activity. Chemogenetic activation of these neurons induces a sex-specific, aberrant pattern of micturition, whereas targeted ablation impairs voluntary marking behavior in response to female cues. We observe multiple regions involved in visceromotor regulation and behavioral state control that project to Bar-Penk neurons, supporting their role as integrators of internal state and environmental context that drive urinary output. These findings provide new insights into the brainstem circuits that shape reflexive and voluntary micturition and highlight how discrete neuronal subtypes contribute to sexually dimorphic regulation of LUT function.

neuroscience↗

bioRxiv2025

American ginseng (Panax quinquefolius L.) extracts (G1899) reverse stress-induced behavioral abnormalities in mice

Stress affects brain functions, which leads to the development of mental disorders like anxiety, depression, cognitive decline, and social dysfunction. There is increasing focus on the role of nutritional, herbal and nutraceutical compounds on mental and cognitive functioning. Interestingly, studies suggest that American ginseng (Panax quinquefolius L.) extracts (G1899) improve cognition. We thus examined whether G1899 showed protective effects on stress-induced behavioral changes in animals. 200 mg/kg G1899 was orally administered daily for 4 weeks to 2-3-month-old female and male mice before inducing stress. To induce acute stress in animals, we intraperitoneally injected a low dose of lipopolysaccharides (LPS) (10 g/kg), and saline was used as a control. We also used chronic restraint stress (CRS) as a chronic stress model in mice. After LPS injection or CRS, multiple behavioral assays were carried out - a sucrose preference test, an open filed test, reciprocal social interaction, contextual fear conditioning, and a tail suspension test - to determine whether acute or chronic stress affected animals behaviors and whether G1899 had protective effects against stress-induced behavioral dysfunction. We found that both LPS injection and CRS induced stress-related behavioral dysfunction, including depression-like behavior, anhedonia, social dysfunction, and fear memory impairments in both females and males. However, G1899 treatment was sufficient to reverse stress-induced behavioral abnormalities in animals. Our data further suggested that G1899 reduced the activity of hippocampal neurons by suppressing glutamatergic activity. Our study suggests that G1899 supplements can be protective against both acute and chronic stress in mice by suppressing neuronal and synaptic activity. HighlightsO_LIAmerican ginseng (Panax quinquefolius L.) extract (G1899) treatment reverses acute stress-induced behavioral dysfunction in mice. C_LIO_LIG1899 treatment reverses chronic stress-induced behavioral dysfunction in mice. C_LIO_LIG1899 treatment reduces serum corticosterone levels in chronically stressed mice. C_LIO_LIG1899 treatment suppresses glutamatergic activity in hippocampal neurons. C_LI

neuroscience↗

bioRxiv2025

Gene syntax defines supercoiling-mediated transcriptional feedback

Gene syntax--the order and arrangement of genes and their regulatory elements--shapes the dynamic coordination of both natural and synthetic gene circuits. Transcription at one locus profoundly impacts the transcription of nearby adjacent genes, but the molecular basis of this effect remains poorly understood. Here, using integrated reporter circuits in human cells, we show that the reciprocal effects of transcription and DNA supercoiling, which we term supercoiling-mediated feedback, regulates expression of adjacent genes in a syntax-specific manner. Using a suite of chromatin state assays, we measure syntax-and induction-dependent formation of chromatin structures in human induced pluripotent stem cells. Applying syntax as a design parameter and without altering sequence or copy number, we built compact gene circuits, tuning the expression mean, noise, and stoichiometry across diverse delivery methods and cell types. Integrating supercoiling-mediated feedback into models of gene regulation will expand our understanding of native systems and enhance the design of synthetic gene circuits.

synthetic biology↗

bioRxiv2024

An AI-Cyborg System for Adaptive Intelligent Modulation of Organoid Maturation

Recent advancements in flexible bioelectronics have enabled continuous, long-term stable interrogation and intervention of biological systems. However, effectively utilizing the interrogated data to modulate biological systems to achieve specific biomedical and biological goals remains a challenge. In this study, we introduce an AI-driven bioelectronics system that integrates tissue-like, flexible bioelectronics with cyber learning algorithms to create a long-term, real-time bidirectional bioelectronic interface with optimized adaptive intelligent modulation (BIO-AIM). When integrated with biological systems as an AI-cyborg system, BIO-AIM continuously adapts and optimizes stimulation parameters based on stable cell state mapping, allowing for real-time, closed-loop feedback through tissue-embedded flexible electrode arrays. Applied to human pluripotent stem cell-derived cardiac organoids, BIO-AIM identifies optimized stimulation conditions that accelerate functional maturation. The effectiveness of this approach is validated through enhanced extracellular spike waveforms, increased conduction velocity, and improved sarcomere organization, outperforming both fixed and no stimulation conditions.

bioengineering↗

bioRxiv2024

Ketamine reverses chronic stress-induced behavioral changes via the expression of Ca2+-permeable AMPA receptors in mice

Background and Purpose: Chronic stress affects brain functions leading to the development of mental disorders like anxiety and depression, as well as cognitive decline and social dysfunction. Among many biological changes in chronically stressed brains, disruptions in AMPA Receptor (AMPAR)-mediated synaptic transmission in the hippocampus are associated with stress responses. We have revealed that low-dose ketamine rapidly induces the expression of GluA1-containing, GluA2-lacking Ca2+-Permeable AMPARs (CP-AMPARs), which enhances glutamatergic synaptic strength in hippocampal neurons. Additionally, subanesthetic low-dose ketamine decreases anxiety- and depression-like behaviors in naive animals. In addition to reducing depression, some research indicates that ketamine may have protective effects against chronic stress in both humans and animals. However, the role of CP-AMPARs in the actions of ketamine's antistress effects is largely unknown. Experimental Approach: We use whole-cell patch-clamp recordings from CA1 pyramidal neurons in female and male hippocampal slices and multiple behavioral assays including reciprocal social interaction, contextual fear conditioning, and tail suspension test. Key Results: We demonstrate that low-dose ketamine treatment reverses chronic restraint stress (CRS)-induced social dysfunction, hippocampus-dependent fear memory loss, and depression-like behavior in both female and male mice. Furthermore, we show that the ketamine-induced antistress effects on these behaviors are dependent on CP-AMPARs. Conclusion and Implications: Our findings suggest that subanesthetic low-dose ketamine rapidly triggers synaptic insertion of CP-AMPARs in the hippocampus, which induces antidepressant and antistress effects.

neuroscience↗

bioRxiv2024

Meta2DB: Curated Shotgun Metagenomic Feature Sets and Metadata for Health State Prediction

Meta2DB is a curated metagenomic and metadata database that provides structurally consistent microbiome taxonomy feature count tables for 13,897 samples across 84 studies, 23 disease states, and 34 geographical locations. All samples were uniformly processed using a streamlined metagenomic classification pipeline that employs a reference database indexed to contain all sequences across all kingdoms of life that were present in the NCBI Nucleotide (nt) database retrieved on Jan 04, 2023. This pipeline leverages high-performance computing (HPC) resources at Lawrence Livermore National Laboratory and was used to process 50TB of publicly available raw metagenomic sequence data. Extensive metadata curation was carried out through a combination of manual curation and automated parsing, producing a consistent inter-study metadata table specifically structured to facilitate training of ML models for prediction of human health.

microbiology↗

bioRxiv2024

Mycobacterium tuberculosis overcomes phosphate starvation by extensively remodelling its lipidome with phosphorus-free lipids

Tuberculosis (TB) is the biggest cause of death from infectious disease worldwide [1-4]. The causative agent, Mycobacterium tuberculosis (Mtb), possesses a complex cell envelope that determines many of the key physiologic and virulence properties that facilitate infection, which comprises multiple classes of unique lipids [5-7]. The macrophage phagosome is a key reservoir of infection in pulmonary TB and multiple studies have shown that inorganic phosphate (Pi) is limiting in this environment [8-11]. The ability of Mtb to sense and respond to phosphate starvation is required for virulence in animal models and replication in human macrophages in vitro [12-14]. Here, we show that during Pi restriction the Mtb lipidome is markedly remodelled such that phospholipids are replaced with multiple classes of phosphorus-free lipids, some of which have not been documented before. Further, we discover that Mtb can metabolise phospholipid polar heads derived from host pulmonary surfactant as an alternative phosphate source, which sustains cell division for several generations during Pi restriction. These dual manipulations of phospholipid metabolism provide Mtb with an escape from phosphate restriction specific to the infection of alveolar macrophages, one of the earliest steps in establishing pulmonary tuberculosis. The changes in envelope lipidome remodelling, akin to that observed in some marine and terrestrial bacteria [15-20] suggests that standard Mtb culture conditions that use media with high concentrations of Pi do not reflect the physiologic environment during infection, thereby potentially undermining vaccine and drug development for tuberculosis. Moreover, the distinct Mtb phosphate-free lipids and the metabolic pathways that generate them could provide new antibiotic targets.

microbiology↗

bioRxiv2024

Development of the Follow-Up Discourse Observation Protocol (FUDOP) for characterizing instructor active-learning follow-up behaviors

Instructors can provide feedback to their class in multiple ways. One way is through their follow-up behaviors, which are the specific strategies instructors implement after active learning activities. These behaviors could play an important role in student learning as students can receive feedback from the instructor. However, there is little research on the effects of different types of follow-up behaviors. Follow-up after active learning can be seen as a form of discourse between the instructor and the entire class. Previous researchers developed the Classroom Discourse Observation Protocol (CDOP) to analyze discourse between the instructor and individual students or small groups. We used CDOP as a starting point to develop and validate a new protocol, the Follow-Up Discourse Observation Protocol (FUDOP), to characterize instructional follow-up behaviors to the entire class after active-learning activities. We then used FUDOP to characterize follow-up behaviors of multiple instructors in introductory biology courses at three different universities. We measured consistent differences in these behaviors across instructors but not within instructors, demonstrating that instructors may engage in consistent follow-up behaviors. FUDOP could allow instructors and researchers to better measure and analyze follow-up behaviors and their effects, which could in turn provide guidance to instructors and faculty developers.

scientific communication and education↗

bioRxiv2024

Co-activation of selective nicotinic acetylcholine receptor subtypes is required to reverse hippocampal network dysfunction and prevent fear memory loss in Alzheimer's disease

Beta-amyloid peptide (A{beta})-induced suppression of hippocampal GABAergic interneuron activity drives hyperexcitability, amyloid pathology, and cognitive impairment in Alzheimers disease (AD), suggesting that enhancing hippocampal inhibition may be protective. However, hippocampal interneurons are highly diverse and differentially regulate inhibition and cognition, making it challenging to identify the affected subtypes and optimally restore hippocampal inhibition in AD. We have previously found that A{beta} selectively binds to two of the three major hippocampal nicotinic acetylcholine receptor (nAChR) subtypes, 7- and 4{beta}2-nAChRs, but not 3{beta}4-nAChRs, and inhibits these two receptors in hippocampal inhibitory interneurons to decrease their activity, leading to hyperexcitation in excitatory neurons. Here, we further reveal that 7- and 4{beta}2-nAChRs predominantly control the nicotinic cholinergic signaling and neuronal activity in hippocampal parvalbumin-positive (PV+) and somatostatin-positive (SST+) inhibitory interneurons, respectively. We also find that systemic co-stimulation of 7- and 4{beta}2-nAChRs is required to reverse hippocampal hyperexcitability, dysfunction of fear learning-associated hippocampal oscillatory activity, and hippocampus-dependent memory loss and reduce A{beta} pathology in AD model mice. This suggests that co-stimulation of PV+ and SST+ cells via activation of 7- and 4{beta}2-nAChRs together is required to enhance hippocampal inhibition optimally, which reverses hippocampal dysfunction, reduces amyloid pathology, and ultimately prevents memory loss in AD. Significance StatementDevelopment of a safe and effective unified strategy to counteract hyperexcitability holds a significant promise in advancing Alzheimers disease (AD) treatment. Studies suggest that beta-amyloid peptide (A{beta}) is a major trigger of hyperexcitability. However, the mechanisms of how A{beta} could participate in hyperexcitability are still not fully understood. Here, we reveal that A{beta} inhibits distinct hippocampal nicotinic acetylcholine receptor (nAChR) subtypes in different hippocampal inhibitory interneuron subtypes, which leads to hyperexcitability, resulting in amyloid pathology and memory loss in AD. We further discover that systemic co-stimulation of these nAChRs is required for neuroprotection against AD at the cellular, circuit, network, and behavioral levels. Identifying this mechanism can thus provide a new therapeutic strategy in AD.

neuroscience↗

bioRxiv2024

Development and Utilization of 3D Anatomy Education Content using Metaverse and XR for Remote Telemedicine Education

The objective of this study is to explore innovative integration within the field of anatomy education by leveraging HoloLens 2 Augmented Reality Head-Mounted Display (AR HMD) technology and real-time cloud rendering. Initial 3D datasets, comprising extensive anatomical information for each bone, were obtained through the 3D scanning of a full-body cadaver of Korean male origin. Subsequently, these datasets underwent refinement processes aimed at enhancing visual fidelity and optimizing polygon counts, utilizing Blender software. Unity was employed for the development of the Metaverse platform, incorporating tailored 3D User Experience (UX) and User Interface (UI) components to facilitate interactive anatomy education via imported cadaver models. Integration with real-time remote rendering cloud servers, such as Azure, was implemented to augment the performance and rendering capabilities of the HoloLens 2 AR HMD. The extended reality (XR) content uses the Photon Cloud network for real-time data synchronization and HoloLens 2 voice functionality. The metaverse platform supports user interaction through room creation and joining, with various tools for bone manipulation, color differentiation, and surface output. Collaboration features enable sharing and synchronization of model states. The study highlights the importance of technological innovation in anatomy education for future medical professionals. The proposed content aims to address limitations of traditional methods and enhance learning experiences. Continued efforts in developing and improving such technologies are crucial to equip learners with essential skills for adaptation in the evolving healthcare landscape. keyword: Metaverse, Anatomy, Cadaver, Extended Reality(XR), Virtual Reality(VR)

scientific communication and education↗

bioRxiv2024

Cancer-associated DNA Hypermethylation of Polycomb Targets Requires DNMT3A Dual Recognition of Histone H2AK119 Ubiquitination and the Nucleosome Acidic Patch

During tumor development, promoter CpG islands (CGIs) that are normally silenced by Polycomb repressive complexes (PRCs) become DNA hypermethylated. The molecular mechanism by which de novo DNA methyltransferase(s) catalyze CpG methylation at PRC-regulated regions remains unclear. Here we report a cryo-EM structure of the DNMT3A long isoform (DNMT3A1) N-terminal region in complex with a nucleosome carrying PRC1-mediated histone H2A lysine 119 monoubiquitination (H2AK119Ub). We identify regions within the DNMT3A1 N-terminus that bind H2AK119Ub and the nucleosome acidic patch. This bidentate interaction is required for effective DNMT3A1 engagement with H2AK119Ub-modified chromatin in cells. Furthermore, aberrant redistribution of DNMT3A1 to Polycomb target genes inhibits their transcriptional activation during cell differentiation and recapitulates the cancer-associated DNA hypermethylation signature. This effect is rescued by disruption of the DNMT3A1-acidic patch interaction. Together, our analyses reveal a binding interface critical for countering promoter CGI DNA hypermethylation, a major molecular hallmark of cancer.

cancer biology↗

bioRxiv2024

A CANCER PERSISTENT DNA REPAIR CIRCUIT DRIVEN BY MDM2, MDM4 (MDMX), AND MUTANT P53 FOR RECRUITMENT OF MDC1 AND 53BP1 TO CHROMATIN

The influence of the metastasis promoting proteins mutant p53 (mtp53) and MDM2 on Cancer Persistent Repair (CPR) to promote cancer cell survival is understudied. Interactions between the DNA repair choice protein 53BP1 and wild type tumor suppressor protein p53 (wtp53) regulates cell cycle control. Cancer cells often express elevated levels of transcriptionally inactive missense mutant p53 (mtp53) that interacts with MDM2 and MDM4/MDMX (herein called MDMX). The ability of mtp53 to maintain a 53BP1 interaction while in the context of interactions with MDM2 and MDMX has not been described. We asked if MDM2 regulates chromatin-based phosphorylation events in the context of mtp53 by comparing the chromatin of T47D breast cancer cells with and without MDM2 in a phospho-peptide stable isotope labeling in cell culture (SILAC) screen. We found reduced phospho-53BP1 chromatin association, which we confirmed by chromatin fractionation and immunofluorescence in multiple breast cancer cell lines. We used the Proximity Ligation Assay (PLA) in breast cancer cell lines and detected 53BP1 in close proximity to mtp53, MDM2, and the DNA repair protein MDC1. Through disruption of the mtp53-MDM2 interaction, by either Nutlin 3a or a mtp53 R273H C-terminal deletion, we uncovered that mtp53 was required for MDM2-53BP1 interaction foci. Our data suggests that mtp53 works with MDM2 and 53BP1 to promote CPR and cell survival.

cancer biology↗

bioRxiv2023

Integrative multiomics analysis of neointima proliferation in human saphenous vein: implications for bypass graft disease

IntroductionHuman saphenous veins (SV) are widely used as grafts in coronary artery bypass (CABG) surgery but often fail due to neointima proliferation (NP). NP involves complex interplay between vascular smooth muscle cells (VSMC) and fibroblasts. Little is known, however, regarding the transcriptomic and proteomic dynamics of NP. Here, we performed multi-omics analysis in an ex vivo tissue culture model of NP in human SV procured for CABG surgery. Methods and resultsHistological examination demonstrated significant elastin degradation and NP (indicated by increased neointima area and neointima/media ratio) in SV subjected to tissue culture. Analysis of data from 73 patients suggest that the process of SV adaptation and NP may differ according to sex and body mass index. RNA sequencing confirmed upregulation of pro-inflammatory and proliferation-related genes during NP and identified novel processes, including increased cellular stress and DNA damage responses, which may reflect tissue trauma associated with SV harvesting. Proteomic analysis identified upregulated extracellular matrix-related and coagulation/thrombosis proteins and downregulated metabolic proteins. Spatial transcriptomics detected transdifferentiating VSMC in the intima on the day of harvesting and highlighted dynamic alterations in fibroblast and VSMC phenotype and behavior during NP. Specifically, we identified new cell subpopulations contributing to NP, including SPP1+, LGALS3+ VSMC and MMP2+, MMP14+ fibroblasts. ConclusionDynamic alterations of gene and protein expression occur during NP in human SV. Identification of the human-specific molecular and cellular mechanisms may provide novel insight into SV bypass graft disease.

genomics↗

bioRxiv2023

A Modified BPaL Regimen for Tuberculosis Treatment replaces Linezolid with Inhaled Spectinamides

The Nix-TB clinical trial evaluated a new 6-month regimen containing three-oral- drugs; bedaquiline (B), pretomanid (Pa) and linezolid (L) (BPaL regimen) for treatment of tuberculosis (TB). This regimen achieved remarkable results as almost 90% of the multidrug resistant (MDR) or extensively drug resistant (XDR) TB participants were cured but many patients also developed severe adverse events (AEs). The AEs were associated with the long-term administration of the protein synthesis inhibitor linezolid. Spectinamide 1599 is also a protein synthesis inhibitor of Mycobacterium tuberculosis with an excellent safety profile but which lacks oral bioavailability. Here, we propose to replace L in the BPaL regimen with spectinamide (S) administered via inhalation and we demonstrate that inhaled spectinamide 1599, combined with BPa --BPaS regimen--has similar efficacy to that of BPaL regimen while simultaneously avoiding the L-associated AEs. The BPaL and BPaS regimens were compared in the BALB/c and C3HeB/FeJ murine chronic TB efficacy models. After 4-weeks of treatment, both regimens promoted equivalent bactericidal effect in both TB murine models. However, treatment with BPaL resulted in significant weight loss and the complete blood count suggested development of anemia. These effects were not similarly observed in mice treated with BPaS. BPaL and BPa, but no the BPaS treatment, also decreased myeloid to erythroid ratio suggesting the S in the BPaS regimen was able to recover this effect. Moreover, the BPaL also increased concentration of proinflammatory cytokines in bone marrow compared to mice receiving BPaS regimen. During therapy both regimens improved the lung lesion burden, reduced neutrophil and cytotoxic T cells counts while increased the number of B and helper and regulatory T cells. These combined data suggest that inhaled spectinamide 1599 combined with BPa is an effective TB regimen that avoids L-associated AEs. IMPORTANCETuberculosis (TB) is an airborne infectious disease that spreads via aerosols containing Mycobacterium tuberculosis (Mtb), the causative agent of TB. TB can be cured by administration of 3-4 drugs for 6-9 months but there are limited treatment options for patients infected with multidrug (MDR) and extensively resistant (XDR) strains of Mtb. BPaL is a new all-oral combination of drugs consisting of Bedaquiline (B), Pretomanid (Pa) and Linezolid (L). This regimen was able to cure [~]90% of MDR and XDR TB patients in clinical trials but many patients developed severe adverse events (AEs) associated to the long-term administration of linezolid. We evaluated a new regimen in which Linezolid in the BPaL regimen was replaced with inhaled spectinamide 1599. In the current study, we demonstrate that 4-weeks of treatment with inhaled spectinamide 1599 in combination with Bedaquiline and Pretomanid has equivalent efficacy to the BPaL drug combination and avoids the L-associated-AEs.

microbiology↗

bioRxiv2023

The small molecule CBR-5884 inhibits the Candida albicans phosphatidylserine synthase

Systemic infections by Candida spp. are associated with high mortality rates, partly due to limitations in current antifungals, highlighting the need for novel drugs and drug targets. The fungal phosphatidylserine synthase, Cho1, from Candida albicans is a logical antifungal drug target due to its importance in virulence, absence in the host and conservation among fungal pathogens. Inhibitors of Cho1 could serve as lead compounds for drug development, so we developed a target-based screen for inhibitors of purified Cho1. This enzyme condenses serine and cytidyldiphosphate-diacylglycerol (CDP-DAG) into phosphatidylserine (PS) and releases cytidylmonophosphate (CMP). Accordingly, we developed an in vitro nucleotidase-coupled malachite green-based high throughput assay for purified C. albicans Cho1 that monitors CMP production as a proxy for PS synthesis. Over 7,300 molecules curated from repurposing chemical libraries were interrogated in primary and dose-responsivity assays using this platform. The screen had a promising average Z score of [~]0.8, and seven compounds were identified that inhibit Cho1. Three of these, ebselen, LOC14, and CBR-5884, exhibited inhibitory effects against C. albicans cells, with fungicidal inhibition by ebselen and fungistatic inhibition by LOC14 and CBR-5884. Only CBR-5884 showed evidence of disrupting in vivo Cho1 function by inducing phenotypes consistent with the cho1{Delta}{Delta} mutant, including a reduction of cellular PS levels. Kinetics curves and computational docking indicate that CBR-5884 competes with serine for binding to Cho1 with a Ki of 1,550 {+/-} 245.6 nM. Thus, this compound has the potential for development into an antifungal compound.

microbiology↗

bioRxiv2023

The CLAMP GA-binding transcription factor regulates heat stress-induced transcriptional repression by associating with 3D loop anchors.

To survive exposure to heat stress (HS), organisms activate stress response genes and repress constitutive gene expression, thereby preventing the accumulation of potentially toxic RNA and protein products. Although many studies have elucidated the mechanisms that drive HS-induced activation of stress response genes across species, little is known about the mechanisms that repress constitutively expressed genes. Using nascent RNA-sequencing, we identify the first reported transcription factor (TF) that regulates repression of constitutive genes upon heat stress across species and define direct and indirect mechanisms of action by integrating 3D genomic approaches. We demonstrate that the CLAMP (Chromatin-linked adaptor for MSL complex proteins) GA-binding transcription factor (TF) regulates [~]75% of the HS-induced repression in Drosophila, a well-established model for understanding the mechanisms of HS-induced gene regulation. Using Micro-C, we demonstrate that heat stress induces widespread changes in local 3D chromatin looping, which are significantly associated with HS-induced transcriptional changes. Overall, we identify CLAMP as the first reported TF that induces HS repression, which modulates 3D chromatin looping through both direct mechanisms and indirect mechanisms. Moreover, we present the highest-resolution heat stress 3D genomic dataset available in Drosophila, providing a key resource for generating mechanistic insights into how temperature regulates 3D genomic contacts.

genomics↗