Biology subjects

Lee, J.

Publications and source records attributed to Lee, J..

At least 325 records · Page 18Linked to original sources

bioRxiv2024

Effects of Age and Cognitive Functions on the Neural Tracking of Speech in Noise

Older adults often struggle to comprehend speech in noisy environments, a challenge influenced by declines in both auditory processing and cognitive functions. This study examines age-related differences in speech recognition in noise, focusing on the roles of delta (1-4 Hz) and theta (4-8 Hz) neural oscillations and their relationship with cognitive function, particularly working memory. Electroencephalography (EEG) was used to collect data from 23 young adults (20-35 years) and 23 older adults (65-80 years) with normal hearing. Cognitive assessments were administered to older adults, and both groups completed an EEG task involving speech recognition in Speech-Shaped Noise (SSN) at individualized noise levels based on their Sentence Recognition Scores (SRS). Results showed that age significantly impacted hit rates and reaction times in noisy speech recognition tasks. Theta-band neural tracking was notably stronger in older adults, while delta-band tracking showed no age-related difference. Pearsons correlations indicated significant associations between age-related cognitive decline, reduced hearing sensitivity, and Mini-Mental State Examination (MMSE) scores. Regression analyses showed that theta-band neural tracking at specific SRS levels significantly predicted word list recognition in the higher SRT group, while constructional recall was strongly predicted in the lower SRT group. The findings suggest that older adults may rely on theta-band neural tracking as a compensatory mechanism to support speech perception in noise, with indirect links between working memory and speech perception. Further research is needed to explore the causal relationship between cognitive function and hearing.

neuroscience↗

bioRxiv2024

Leveraging Drosophila Models to Explore AI-generated Synthetic Peptide's Potential in Boosting Honeybee Health and Resilience

The integration of artificial intelligence (AI) and machine learning (ML) in peptide design has revolutionized the development of antimicrobial peptides (AMPs), which are essential components of innate immunity. In this study, we identified a novel synthetic peptide, PAN4 (GAYTFKIRRK), through genetic screening of AI-generated candidates in Drosophila melanogaster. PAN4 demonstrated robust antimicrobial activity, stress tolerance, and antitumor effects, significantly enhancing survival rates following bacterial infections and improving locomotor behaviors without adversely affecting lifespan. Furthermore, PAN4 expression in intestinal stem cells completely suppressed RasV12-induced tumor progression, indicating its potential role in cancer prevention. The peptide also mitigated gut barrier dysfunction associated with sleep deprivation and reduced inflammation in a dextran sulfate sodium (DSS)-induced colitis model. Mechanistically, PAN4s antimicrobial activity was linked to its interaction with specific peptidoglycan recognition proteins (PGRPs), particularly PGRP-SC1a, while the Tak1-mediated immune signaling pathway was found to be non-essential for its efficacy. PAN4 showed promising effects on honeybee health, enhancing survival rates under bacterial stress. Furthermore, PAN4 expression demonstrated significant anti-tumor activity in the Drosophila gut tumor model. Our findings suggest that PAN4 serves as a versatile agent with significant implications for enhancing immune responses and combating diseases in honeybee populations, paving the way for future applications in agriculture and medicine.

genetics↗

bioRxiv2024

Identification of neuron-glia signaling feedback in human schizophrenia using patient-derived, mix-and-match forebrain assembloids

Although abnormal activities across multiple cell types are believed to contribute to the development of various neurodevelopmental disorders, current brain organoid technologies fall short in accurately modeling the dynamic cellular interactions in the human brain. Recently, we developed a cellular reconstitution technology to create human forebrain assembloids with enhanced cellular diversity, representing dynamic interactions between neurons and glial cells. Here, we created patient-derived, mix-and-match forebrain assembloids, in which neurons, astrocytes, and microglia from both healthy individuals and schizophrenia patients were reconstituted in a combinatorial manner, and identified aberrant cellular interactions between neurons and glial cells in human schizophrenia. At the early stage, schizophrenia forebrain assembloids showed premature neurogenesis induced by the abnormal proliferation and differentiation of neural progenitor cells. Integrated modular analysis of gene expression in post-mortem schizophrenia brain tissue and brain assembloids found increased expression of tumor protein p53 (TP53) and nuclear factor of activated T-cells 4 (NFATC4), which functioned as master transcriptional regulators to epigenetically reprogram the transcriptome involved in the cellular dynamics of neuronal progenitor cells, leading to premature neurogenesis. At the later stage, we observed weakened structures of laminar organization of the cortical layers in forebrain assembloids and identified the neuron-dependent transcriptional plasticity of glial cells and their altered signaling feedback with neurons, in which neuronal urocortin (UCN) and protein tyrosine phosphatase receptor type F (PTPRF) elicited the expression of Wnt family member 11 (WNT11) and thrombospondin 4 (THBS4) in astrocytes and microglia, respectively. These aberrant signaling axes altered the neuronal transcriptome associated with neuronal response to various stimuli and synthetic processes of biomolecules, resulting in reduced synapse connectivity. Thus, we elucidated developmental stage-specific, multifactorial mechanisms by which dynamic cellular interplay among neural progenitor cells, neurons, and glial cells contribute to the development of the human schizophrenia brain. Our study further demonstrated the potential and applicability of patient-derived forebrain assembloid technology to advance our understanding of the pathogenesis of various neurodevelopmental disorders.

neuroscience↗

bioRxiv2024

A Co-essentiality Network of Cancer Driver Genes Better Prioritizes Anticancer Drugs

Diverse molecular networks have been extensively studied to discover therapeutic targets and repurpose approved drugs. However, it is necessary to select a suitable network since the performance of network medicine relies heavily on the completeness and characteristics of the selected network. Although a network using gene essentiality from cancer cells could be an effective platform for identifying anticancer targets, efforts to apply these networks in therapeutic applications have been limited. We constructed a phenotype-level network using the co-essentiality relationship between genes in CRISPR screens across 769 cancer cells to discover therapeutic targets for diverse cancer types. Leveraging cancer driver genes and network propagation on the networks, we found that the co-essentiality network better prioritized anticancer targets and biomarkers and predicted more precise drug responses in cancer cells than other molecular networks. The co-essentiality network outperformed conventional molecular networks in drug repurposing, which were validated in silico by clinical trial records. Notably, the co-essentiality network provided 37 repurposed drugs that the other networks have yet to cover, and we showcased three approved drugs repurposed for lung adenocarcinoma (Pioglitazone hydrochloride, Atovaquone, and Eflornithine). Our study provides a novel network for precision oncology to improve the identification of therapeutic targets in specific cancers.

bioinformatics↗

bioRxiv2024

SpaceExpress: a method for comparative spatial transcriptomics based on intrinsic coordinate systems of tissues

Spatial transcriptomics (ST) technologies have enabled new explorations into the spatial organization of tissues and their functional implications. However, one of the most fundamental analyses - comparative analysis of spatial gene expression across phenotypes - remains a formidable challenge. We introduce SpaceExpress, a novel statistical tool for detecting phenotype-associated changes in spatial expression patterns. SpaceExpress employs a neural network to embed multiple ST samples in a common latent space, enabling robust cross-sample comparisons despite structural and technical variations. It then uses spline regression to test differential spatial expression of genes between conditions, identifying specific regions of the tissue where expression patterns diverge and quantifying the magnitude of those differences, with rigorous false discovery control and handling of multiple replicates per condition. It includes visualization tools to help interpret spatial pattern differences. We demonstrate the tools effectiveness on synthetic and real ST datasets, revealing mechanistic insights into behavior- and development-related neurogenomic changes in honey bees and mice. Our work extends the highly influential paradigm of differential gene expression analysis to spatial omics.

bioinformatics↗

bioRxiv2024

Integrated analysis of COVID-19 multi-omics data for eQTLs reveals genetic mechanisms underlying disease severity

The global pandemic caused by the SARS-CoV-2 virus provided an unprecedented opportunity to investigate genetic factors influencing the disease severity of the viral infection. Despite a plethora of recent research on both SARS-CoV-2 and COVID-19, few have taken a systems biology approach to address individual-level variation, especially based on non-European populations. Accordingly, we analyzed multi-omics data generated at three timepoints from 193 Korean COVID-19 patients with mild or severe symptoms, composed of whole genome sequencing, blood-based single-cell RNA-sequencing (2.15M cells), 195 cytokine profiles, and human leukocyte antigen (HLA) allele data. We identified expression quantitative trait loci (eQTLs), disease severity interacting eQTLs (n = 388), and disease progression interacting eQTLs (n = 945) for various cell types. We elucidated a complex regulatory mechanism involving HLA genes and their targets, and identified genetic determinants of cytokine levels. Finally, we show how regulation of ieQTLs is established by upstream transcription factors (TFs), illustrating complex regulation of the IGFBP7 ieQTL by a combined action of two TFs, which is potentially important in conferring differential severity. This study illuminates an efficient molecular interrogation framework that can be applied toward understanding infectious disease progression in individuals of different genotypes.

genetics↗

bioRxiv2024

Multi-omics analysis and genome-scale metabolic reconstruction of cattle Bos taurus for optimal production of cultured meat

With the growing urgency of addressing climate change, cultured meat has gained significant attention as a sustainable alternative to conventional meat production. Bos taurus, a key cattle species, is considered as a potential source of cultured meat. However, much remains to be understood about the biology of B. taurus muscle cells. In this study, bovine satellite cells (BSCs) derived from the semimembranosus muscle of Korean Hanwoo cattle were subjected to multi-omics profiling and genome-scale metabolic reconstruction. First, differential gene expression and gene set enrichment analyses, based on RNA-seq data, identified key pathways associated with muscle cell proliferation (e.g., Cell cycle and RNA polymerase) and differentiation (e.g., Cytoskeleton in muscle cells and Tryptophan metabolism). Next, using the human1 GEM as a template, we constructed the first B. taurus-specific genome-scale metabolic model (GEM), named BtaSBML2986, which comprises 2,986 genes, 13,278 reactions, and 8,652 metabolites. Muscle cells were cultured under six distinct conditions, and biomass predictions generated using BtaSBML2986 were validated against experimental growth rates. This integrated approach also provided insights into core pathways such as glycolysis and the TCA cycle. BtaSBML2986 represents a significant step forward in understanding B. taurus muscle metabolism and will serve as a valuable tool for advancing cultured meat research and optimizing culture processes.

systems biology↗

bioRxiv2024

Lymphatic drainage of cerebrospinal fluid using lymph node seeker 64Cu-labeled Gram-negative bacterial extracellular vesicles PET

Cerebrospinal fluid (CSF) is drained into the systemic lymphatics via paravertebral lymph nodes. Superficial and deep cervical lymph nodes collect CSF in mice, but the exact and quantified routes are unknown. Recently, we simultaneously visualized cervical, sacral and iliac lymph nodes via serial imaging on the intrathecal [64Cu]Cu-albumin positron emission tomography. Paravertebral lymph nodes might act as sentinels to monitor the CSF, brain, and spinal cord. We used 64Cu-labeled Escherichia coli extracellular vesicles, outer membrane vesicles (OMVs), as lymph node seekers for intrathecal administration with an optimized volume/rate and quantified the differential amounts of various paravertebral lymph nodes along the axis of the brain and spinal cord in mice. The quantified results revealed 77.3% in superficial and deep cervical lymph nodes, 11.4% in abdominal/pelvic lymph nodes and 11.3% in sacral lymph nodes. Click-labeled [64Cu]Cu-OMVs were drained to reach and stop at the lymph nodes on serial quantification. The cervical lymph nodes drained most of the OMV-laden CSF, which is proportional to the surface areas of the brain (70%) and spinal cord in mice. We propose that all paravertebral lymph nodes monitor the segmental regions of the brain and spinal cord as immediate sentinel lymph nodes against the central nervous system.

neuroscience↗

bioRxiv2024

Humoral correlate of vaccine-mediated protection from tuberculosis identified in humans and non-human primates

Development of an effective tuberculosis (TB) vaccine has been challenged by incomplete understanding of specific factors that provide protection against Mycobacterium tuberculosis (Mtb) and the lack of a known correlate of protection (CoP). Using a combination of samples from a vaccine showing efficacy (DarDar [NCT00052195]) and Bacille Calmette-Guerin (BCG)-immunized humans and nonhuman primates (NHP), we identify a humoral CoP that translates across species and vaccine regimens. Antibodies specific to the DarDar vaccine strain (M. obuense) sonicate (MOS) correlate with protection from the efficacy endpoint of definite TB. In humans, antibodies to MOS also scale with vaccine dose, are elicited by BCG vaccination, are observed during TB disease, and demonstrate cross-reactivity with Mtb; in NHP, MOS-specific antibodies scale with dose and serve as a CoP mediated by BCG vaccination. Collectively, this study reports a novel humoral CoP and specific antigenic targets that may be relevant to achieving vaccine-mediated protection from TB.

immunology↗

bioRxiv2024

MCSPACE: inferring microbiome spatiotemporal dynamics from high-throughput co-localization data

Recent advances in high-throughput approaches for estimating co-localization of microbes, such as SAMPL-seq, allow characterization of the biogeography of the gut microbiome longitudinally and at unprecedented scale. However, these high-dimensional data are complex and have unique noise properties. To address these challenges, we developed MCSPACE, a probabilistic AI method that infers from microbiome co-localization data spatially coherent assemblages of taxa, their dynamics over time, and their responses to perturbations. To evaluate MCSPACEs capabilities, we generated the largest longitudinal microbiome co-localization dataset to date, profiling spatial relationships of microbes in the guts of mice subjected to serial dietary perturbations over 76 days. Analyses of these data and an existing human longitudinal dataset demonstrated superior benchmarking performance of MCSPACE over existing methods, and moreover yielded insights into spatiotemporal structuring of the gut microbiome, including identifying temporally persistent and dynamic microbial assemblages in the human gut, and shifts in assemblages in the murine gut induced by specific dietary components. Our results highlight the utility of our method, which we make available to the community as an open-source software tool, for elucidating dynamics of microbiome biogeography and gaining insights into the role of spatial relationships in host-microbial ecosystem function.

microbiology↗

bioRxiv2024

Investigating the consequences of chronic short sleep for metabolism and survival of oxidative stress

In previous work, we found that short sleep caused sensitivity to oxidative stress; here we set out to characterize the physiological state of a diverse group of chronically short-sleeping mutants during hyperoxia as an acute oxidative stress. Using RNA-sequencing analysis, we found that short-sleeping mutants had a normal transcriptional oxidative stress response relative to controls. In both short-sleeping mutants and controls, hyperoxia led to downregulation of glycolytic genes and upregulation of genes involved in fatty acid metabolism, reminiscent of metabolic shifts during sleep. We hypothesized that short-sleeping mutants may be sensitive to hyperoxia because of defects in metabolism. Consistent with this, short-sleeping mutants were sensitive to starvation. Using metabolomics, we identified a pattern of low levels of long chain fatty acids and lysophospholipids in short-sleeping mutants relative to controls during hyperoxia, suggesting a defect in lipid metabolism. Though short-sleeping mutants did not have common defects in many aspects of lipid metabolism (basal fat stores, usage kinetics during hyperoxia, respiration rates, and cuticular hydrocarbon profiles), they were all sensitive to dehydration, suggesting a general defect in cuticular hydrocarbons, which protect against dehydration. To test the bi-directionality of sleep and lipid metabolism, we tested flies with both diet-induced obesity and genetic obesity. Flies with diet-induced obesity had no sleep or oxidative stress phenotype; in contrast, the lipid metabolic mutant, brummer, slept significantly more than controls but was sensitive to oxidative stress. Previously, all short sleepers tested were sensitive and all long sleepers resistant to oxidative stress. brummer mutants, the first exceptions to this rule, lack a key enzyme required to mobilize fat stores, suggesting that a defect in accessing lipid stores can cause sensitivity to oxidative stress. Taken together, we found that short-sleeping mutants have many phenotypes in common: sensitivity to oxidative stress, starvation, dehydration, and defects in lipid metabolites. These results argue against a specific role for sleep as an antioxidant and suggest the possibility that lipid metabolic defects underlie the sensitivity to oxidative stress of short-sleeping mutants.

physiology↗

bioRxiv2024

Induced B-Cell Receptor Diversity Predicts PD-1 Blockade Immunotherapy Response.

Immune checkpoint inhibitors such as anti-PD-1 antibodies (aPD1) can be effective in treating advanced cancers. However, many patients do not respond and the mechanisms underlying these differences remain incompletely understood. In this study, we profile a cohort of patients with locally-advanced or metastatic basal cell carcinoma undergoing aPD-1 therapy using single-cell RNA sequencing, high-definition spatial transcriptomics in tumors and draining lymph nodes, and spatial immunoreceptor profiling, with long-term clinical follow-up. We find that successful responses to PD-1 inhibition are characterized by an induction of B-cell receptor (BCR) clonal diversity after treatment initiation. These induced BCR clones spatially co-localize with T-cell clones, facilitate their activation, and traffic alongside them between tumor and draining lymph nodes to enhance tumor clearance. Furthermore, we validated aPD1-induced BCR diversity as a predictor of clinical response in a larger cohort of glioblastoma, melanoma, and head and neck squamous cell carcinoma patients, suggesting that this is a generalizable predictor of treatment response across many types of cancers. We discover that pre-treatment tumors harbor a characteristic gene expression signature that portends a higher probability of inducing BCR clonal diversity after aPD-1 therapy, and we develop a machine learning model that predicts PD-1-induced BCR clonal diversity from baseline tumor RNA sequencing. These findings underscore a dynamic role of B cell diversity during immunotherapy, highlighting its importance as a prognostic marker and a potential target for intervention in non-responders.

cancer biology↗

bioRxiv2024

Polyfunctional IL-21+ IFNg+ T follicular helper cells contribute to checkpoint inhibitor diabetes mellitus and can be targeted by JAK inhibitor therapy

Immune checkpoint inhibitors (ICI) have revolutionized cancer therapy, but their use is limited by the development of autoimmunity in healthy tissues as a side effect of treatment. Such immune-related adverse events (IrAE) contribute to hospitalizations, cancer treatment interruption and even premature death. ICI-induced autoimmune diabetes mellitus (ICI-T1DM) is a life-threatening IrAE that presents with rapid pancreatic beta-islet cell destruction leading to hyperglycemia and life-long insulin dependence. While prior reports have focused on CD8+ T cells, the role for CD4+ T cells in ICI-T1DM is less understood. Here, we identify expansion CD4+ T follicular helper (Tfh) cells expressing interleukin 21 (IL-21) and interferon gamma (IFN{gamma}) as a hallmark of ICI-T1DM. Furthermore, we show that both IL-21 and IFN{gamma} are critical cytokines for autoimmune attack in ICI-T1DM. Because IL-21 and IFN{gamma} both signal through JAK-STAT pathways, we reasoned that JAK inhibitors (JAKi) may protect against ICI-T1DM. Indeed, JAKi provide robust in vivo protection against ICI-T1DM in a mouse model that is associated with decreased islet-infiltrating Tfh cells. Moreover, JAKi therapy impaired Tfh cell differentiation in patients with ICI-T1DM. These studies highlight CD4+ Tfh cells as underrecognized but critical mediators of ICI-T1DM that may be targeted with JAKi to prevent this grave IrAE. VISUAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=92 SRC="FIGDIR/small/625710v1_ufig1.gif" ALT="Figure 1"> View larger version (26K): org.highwire.dtl.DTLVardef@ed4acdorg.highwire.dtl.DTLVardef@c9e062org.highwire.dtl.DTLVardef@1aa81eforg.highwire.dtl.DTLVardef@1388747_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

bioRxiv2024

C. elegans huntingtin, htt-1, promotes robust autophagy induction and survival under stress conditions

Huntingtin (HTT) is the gene responsible for Huntingtons disease (HD), a neurodegenerative disorder caused by a CAG trinucleotide repeat expansion mutation. While HD pathogenesis has traditionally been attributed to the toxic gain-of-function effects of mutant huntingtin (mHTT), increasing evidence underscores the critical role of wild-type HTT loss-of-function. Understanding the physiological roles of HTT is essential for elucidating HD mechanisms and developing effective therapeutic strategies. The C. elegans htt-1 gene, an ortholog of human HTT, remains largely uncharacterized. Here, we demonstrate that htt-1 promotes survival under stress conditions that requires autophagy as a defense mechanism. Specifically, we identify intestinal htt-1 as a key regulator of C. elegans survival during Pseudomonas aeruginosa PA14 infection. Our findings reveal that htt-1 functions downstream of the MPK-1/ERK pathway to induce systemic autophagy and enhance host defense during immune challenges. Moreover, expression of wild-type human HTT in htt-1 mutant worms rescues the survival defect during PA14 infection. Expression of mutant human HTT, on the other hand, exacerbates survival deficits, underscoring the conserved function of HTT across species. Additionally, we found that htt-1 affects survival and autophagy under heat shock stress conditions. These results establish htt-1 as a critical regulator of survival and autophagy in response to both pathogenic bacterial infection and thermal stress. Author summaryHuntingtin plays essential roles in selective autophagy across various organisms, including Drosophila, mice, and humans. Notably, the C. elegans huntingtin ortholog, htt-1, remains largely uncharacterized. Here, we describe a novel pro-survival role htt-1 in stress resistance. We show that htt-1 mutants exhibit significantly reduced survival during Pseudomonas aeruginosa infection. Expression of wild-type human HTT rescues the reduced survival of htt-1 mutants, whereas mutant HTT further exacerbates the phenotype. These findings establish C. elegans htt-1 as a valuable model for studying huntingtin biology and its roles in stress resistance. Downregulation of ERK in htt-1 mutants had no additional effect on survival, suggesting that htt-1 functions downstream of ERK. Interestingly, htt-1 mutants display reduced autophagy, indicating that htt-1 functions in the ERK-autophagy signaling cascade during infection. Mechanistically, we propose that htt-1 regulates autophagy at the protein level. HTT-1 remains cytoplasmic, and autophagy-related gene transcripts remain stable, without downregulation, in htt-1 mutants following infection. Additionally, htt-1 mutants exhibit reduced survival and impaired autophagy under heat stress. These results suggest that htt-1 may have a broader role in stress resilience extending beyond immune defense.

cell biology↗

bioRxiv2024

Thermodynamic Parameter Estimation for Modified Oligonucleotides Using Molecular Dynamics Simulations

This study investigates the thermodynamic parameters of 1,300 RNA/DNA hybrid duplexes, including both natural and chemically modified forms, using molecular dynamics (MD) simulations. Modified duplexes consist of phosphorothioate (PS) backbones and 2'-O-methoxyethyl (MOE) modifications, both commonly used in therapeutic oligonucleotides. Hybridization enthalpy and entropy were calculated from MD trajectories using molecular mechanics Poisson-Boltzmann surface area (MMPBSA) and molecular mechanics generalized Born surface area (MMGBSA) approaches. To address discrepancies with experimental data, we established empirical relationships by comparing calculated values with known experimental results of natural hybrid duplexes, then extended these relationships to the entire dataset. The corrected parameters were subsequently used to generate nearest-neighbor (NN) models, allowing for experimentally reliable melting temperature predictions. In this process, MMGBSA demonstrated superior predictive performance with high convergence and consistency for both natural and modified duplexes. Specifically, MMGBSA captured the stabilizing effects of the MOE modification with minimal bias, while MMPBSA exhibited greater variability and limited reliability. These findings highlight the potential of MMGBSA for accurate thermodynamic modeling of both natural and modified nucleic acids, providing a robust framework and experimentally meaningful insights for applications in nucleic acid-based therapeutic design and biotechnology.

biochemistry↗

bioRxiv2024

Downregulation of O-GlcNAcylation enhances etoposide-induced p53-mediated apoptosis in HepG2 human liver cancer cells

Etoposide, an anticancer drug that inhibits topoisomerase II, is commonly used in combination chemotherapy. However, the impact of O-GlcNAcylation regulation on etoposides anticancer effects has rarely been investigated. This study evaluated the effect of etoposide on cellular O-GlcNAcylation and whether modulating this process enhances etoposide-induced apoptosis. O-GlcNAc expression was measured after 24 h of etoposide treatment, and the effect of O-GlcNAc transferase (OGT) inhibition by OSMI-1 on etoposides anticancer activity in HepG2 human liver cancer cells was quantitatively analyzed. Additionally, molecular analyses were used to confirm that the observed effects were mediated by p53-induced apoptosis. Etoposide reduced O-GlcNAcylation in a dose-dependent manner without directly interacting with OGT. Cotreatment with 20 M of OSMI-1 lowered the IC50 value for cell viability by approximately 1.64-fold to 60.68 M and increased the EC50 value for cytotoxicity by around 4.07-fold to 43.41 M. Furthermore, this synergistic effect was linked to the activation of the p53/caspase-3/PARP1 pathway. These findings suggest that downregulating O-GlcNAcylation may enhance the efficacy of etoposide-based chemotherapy and help overcome tumor resistance. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC="FIGDIR/small/626030v2_ufig1.gif" ALT="Figure 1"> View larger version (59K): org.highwire.dtl.DTLVardef@3cb205org.highwire.dtl.DTLVardef@cb686forg.highwire.dtl.DTLVardef@356662org.highwire.dtl.DTLVardef@1d4dc40_HPS_FORMAT_FIGEXP M_FIG Etoposide, a topoisomerase II inhibitor, reduces O-GlcNAcylation in HepG2 liver cancer cells. Further inhibition of O-GlcNAc transferase by OSMI-1 enhanced etoposide-induced apoptosis, lowering the IC50 for viability and increasing the EC50 for cytotoxicity. This synergy was mediated by the p53, caspase-3/7, PARP1 pathway, suggesting that targeting O-GlcNAcylation may improve etoposide efficacy. C_FIG

molecular biology↗

bioRxiv2024

Cross-species Comparison of Ultramafic Rock Bio-accelerated Weathering Performance

Carbon mineralization is a natural process that sequesters atmospheric CO2 by reacting it with cations (e.g., Mg2+, Ca2+) released by weathering of rocks to form solid carbonates. However, this process is too slow to capture the excess CO2 resulting from anthropogenic emissions in time to prevent significant warming of the atmosphere1-3. Additionally, accelerating carbon mineralization process by chemical or mechanical methods has proven prohibitively expensive to date4. Microbial rock-dissolution processes, including acidolysis, redoxolysis, and complexolysis, have the potential to accelerate weathering with low energy input5. However, there is no industrially useful microbe capable of dissolving ultramafic (rich in ferromagnesian minerals) rocks, suggesting that one will need to be discovered or built with synthetic biology. While microbes are known to dissolve ultramafic minerals6,7, the performance envelopes for these processes remain uncharacterized, and significant gaps exist in our knowledge of microbe-mineral interaction processes. Here, we make a normalized performance comparison of the dissolution of the ultramafic rock dunite (> 90% olivine ((Mg, Fe)2SiO4)) by three well-known mineral-dissolving microbes: Gluconobacter oxydans7-9, Sphingomonas desiccabilis10,11, and Penicillium simplicissimum12-14. We show that G. oxydans outperformed P. simplicissimum and S. desiccabilis, producing the most acidic biolixiviant (pH 2.15 when leaching 1% pulp density), and extracting the most magnesium (3,130 mg/L when leaching at 3% pulp density). Additionally, G. oxydans co-dissolves nine other metals, eight of which are critical for energy technologies (Cr, Mn, Co, Ni, Cu, and Zn)15,16 with a maximum dissolved concentration of 33 mg/L for Ni. While increasing the pulp density of the dunite (solid to liquid ratio) resulted in higher metal dissolution by G. oxydans and S. desiccabilis, notably pulp densities above 2% inhibited mineral dissolution by P. simplicissimum. Our results provide evidence that the gap in performance between G. oxydans and the other two microbes increases with pulp density, and thus, G. oxydans is best suited for process and genetic engineering to maximize performance and minimize costs and environmental impacts of bio-accelerated weathering. Finally, we propose that G. oxydans and P. simplicissimum can use cellulosic hydrolysate as a cost-effective substitute for glucose for biolixiviant production.

bioengineering↗

bioRxiv2024

Aspergillus nidulans Transcription Factor BrlA is Utilized in a Conidiation-Independent Response to Cell-Wall Stress

Under synchronized conidiation, over 2500 gene products show differential expression, including transcripts for both brlA and abaA, which increase steadily over time. In contrast, during wall-stress induced by the echinocandin micafungin, the brlA transcript is upregulated while the abaA transcript is not. In addition, when mpkA (last protein kinase in the cell wall integrity signaling pathway) is deleted, brlA expression is not upregulated in response to wall stress. Together, these data imply BrlA may play a role in a cellular stress-response which is independent of the canonical BrlA-mediated conidiation pathway. To test this hypothesis, we performed a genome-wide search and found 332 genes with a putative BrlA response element (BRE) in their promoter region. From this set, we identified 28 genes which were differentially expressed in response to wall-stress, but not during synchronized conidiation. This set included seven gene products whose homologues are involved in transmembrane transport and 14 likely to be involved in secondary metabolite biosynthesis. We selected six of these genes for further examination and find that they all show altered expression behavior in the brlA deletion strain. Together, these data support the idea that BrlA plays a role in various biological processes outside asexual development. ImportanceThe Aspergillus nidulans transcription factor BrlA is widely accepted as a master regulator of conidiation. Here, we show that in addition to this function BrlA appears to play a role in responding to cell-wall stress. We note that this has not been observed outside A. nidulans. Further, BrlA-mediated conidiation is highly conserved across Aspergillus species, so this new functionality is likely relevant in other Aspergilli. We identified several transmembrane transporters that have altered transcriptional responses to cell-wall stress in a brlA deletion mutant. Based on our observation, together with what is known about the brlA gene locus regulation, we identify brlA{beta} as the likely intermediary in function of brlA in the response to cell-wall stress.

cell biology↗