Biology subjects

Lee, G.

Publications and source records attributed to Lee, G..

At least 55 records · Page 3Linked to original sources

bioRxiv2024

Discovery and Synthesis of GS-7682, a Novel Prodrug of a 4'-CN-4-Aza-7,9-Dideazaadenosine C-Nucleoside with Broad-Spectrum Potency Against Pneumo- and Picornaviruses and Efficacy in RSV-Infected African Green Monkeys.

Acute respiratory viral infections (ARVI), such as pneumovirus and respiratory picornavirus infections, exacerbate disease in COPD and asthma patients. A research program targeting respiratory syncytial virus (RSV) led to the discovery of GS-7682 (1) a novel phosphoramidate prodrug of a 4'-CN-4-aza-7,9-dideazaadenosine C-nucleoside GS-646089 (2) with broad antiviral activity against RSV EC50 = 3-46 nM, human metapneumovirus (hMPV) EC50 = 210 {+/-} 50 nM, human rhinovirus (RV) EC50 = 54-61 nM, and enterovirus (EV) EC50 = 83-90 nM. Prodrug optimization for cellular potency and lung cell metabolism identified the 5-methyl((S)-hydroxy(phenoxy)phosphoryl)-L-alaninate in combination with 2,3-diisobutyrate promoieties as optimal for high intracellular triphosphate formation in vitro and in vivo. 1 demonstrated significant reductions of viral loads in the lower respiratory tract of RSV-infected African green monkeys when administered once daily via intratracheal nebulized aerosol. Together these finding support additional evaluation of 1 and its analogs as a potential therapeutic for pneumo- and picornaviruses.

biochemistry↗

bioRxiv2024

Mosaic display of stable hemagglutinin monomers induces broad immune responses

The nature of the interplay between immunity and viral variation is infinitely adaptive. Infection frequently induces immune responses against variation-prone epitopes, rather than against spatially hidden conserved epitopes. It thus remains a substantial challenge to elicit the immune responses to the conserved epitopes providing broad-spectrum immunity. We developed an approach of scaffold-mediated mosaic display to present monomeric influenza virus hemagglutinins (HAs), which exposes highly conserved stem and interface epitopes. Stable monomers were rationally engineered from H1 and H3 subtypes and B type HA trimers, with amino acid mutations at the monomer-monomer interface and for disulfide bond formation, and fused to a self-assembling scaffold, to generate a mosaic HA monomer-displaying nanoparticle, 3HA-np. Immunization with 3HA-np induced broadly neutralizing antibodies (bnAbs) in mice and ferrets and protected against challenges with H1N1 and H3N2 viruses. Competitive immunoassays revealed that 3HA-np induced high interface- and stem-binding Ab titers as compared to head Ab titers, indicating that the monomeric and mosaic nature of 3HA-np elicit cross-reactive Abs. Our results suggest that exposure of the hidden conserved epitope by monomer-displaying nanoparticles is a promising approach to generate a universal influenza vaccine.

bioengineering↗

bioRxiv2024

CHANGE-seq-BE enables simultaneously sensitive and unbiased in vitro profiling of base editor genome-wide activity

Base editors (BE) enable programmable conversion of nucleotides in genomic DNA without double-stranded breaks and have substantial promise to become new transformative genome editing medicines. Sensitive and unbiased detection of base editor off-target effects is important for identifying safety risks unique to base editors and translation to human therapeutics, as well as accurate use in life sciences research. However, current methods for understanding the global activities of base editors have limitations in terms of sensitivity or bias. Here we present CHANGE-seq-BE, a novel method to directly assess the off-target profile of base editors that is simultaneously sensitive and unbiased. CHANGE-seq-BE is based on the principle of selective sequencing of adenine base editor modified genomic DNA in vitro, and provides an accessible, rapid, and comprehensive method for identifying genome-wide off-target mutations of base editors.

genomics↗

bioRxiv2024

Induction of expansion of ex vivo NK cells using a new feeder cell built in Brazil. An extended flow cytometry evaluation of K562.mbIL21.4BBL

BackgroundNatural killer (NK) cells are lymphocytes from the innate immune system capable of promoting an antitumor response through activation and inhibition receptors. NK cells can better mediate cell engraftment after hematopoietic stem cell transplantation (HSCT), decreasing relapse rates and preventing viral diseases after HSCT. These characteristics make NK cells eligible for application in cell therapy by increasing the frequency of NK cells in peripheral blood. Manufacturing and using feeder cells is necessary to expand NK cells while keeping their cytotoxic characteristics. AimsWe aimed to develop feeder cells from a K562 leukemic cell line capable of promoting clonal expansion of NK cells ex vivo while preserving its antitumor potential. Methods and resultsFeeder cells, named K562.clone1, were produced by transduction of mbIL-21 and 4-1BBL proteins. Next, peripheral blood NK cells were co-cultivated with K562.clone1 and expanded more than 100 folds compared to NK cells co-cultivated with K562-WT (less than 10 folds). On the first day of cultivation, the average frequency of NK cells (CD3-CD56+CD16+/-) was 5.95% {+/-} 3.92%, increasing to 83.97% {+/-} 8.19% on the fourteenth day after co-cultivation with K562.Clone1, while the percentage of NK cells raised to 75.15% {+/-} 7.57% when co-cultivated with control. In addition, NK cells expanded with the feeder K562.Clone1 were potentially cytotoxic against acute myeloid leukemia (AML) blast, tumor cell lines of leukemia and glial origin. ConclusionWe successfully built a national feeder cell, named K562.Clone1. The co-culture with K562.Clone1 feeder cell, preserving their primordial functions such as missing-self, important to distinguish health and defective cell, and natural cytotoxicity against tumoral cells, and increasing the natural cytotoxicity.

cancer biology↗

bioRxiv2024

Development of radial frequency pattern perception in macaque monkeys

Infant primates see poorly, and most perceptual functions mature steadily beyond early infancy. Behavioral studies on human and macaque infants show that global form perception, as measured by the ability to integrate contour information into a coherent percept, improves dramatically throughout the first several years after birth. However, it is unknown when sensitivity to curvature and shape emerges in early life. We studied the development of shape sensitivity in eighteen macaques, aged 2 months to 10 years. Using radial frequency stimuli (RFS), circular targets whose radii are modulated sinusoidally, we tested monkeys ability to discriminate RFS from circles as a function of the depth and frequency of sinusoidal modulation. We implemented a new 4-choice oddity task and compared the resulting data with that from a traditional 2-alternative task. Behavioral performance at all radial frequencies improved with age. Performance was better for higher radial frequencies, suggesting the developing visual system prioritizes processing of fine visual details that are ecologically relevant. By utilizing two complementary methods, we were able to capture a comprehensive developmental trajectory for shape perception.

neuroscience↗

bioRxiv2024

Transcriptomic and epigenetic responses shed light on soybean resistance to Phytophthora sansomeana

Phytophthora root rot caused by oomycete pathogens in the Phytophthora genus poses a significant threat to soybean productivity. While resistance mechanisms against Phytophthora sojae have been extensively studied in soybean, the molecular basis underlying immune responses to Phytophthora sansomeana remains unclear. We investigated transcriptomic and epigenetic responses of two resistant (Colfax and NE2701) and two susceptible (Williams 82 and Senaki) soybean lines at four time points (2, 4, 8, and 16 hours post inoculation, hpi) after P. sansomeana inoculation. Comparative transcriptomic analyses revealed a greater number of differentially expressed genes (DEGs) upon pathogen inoculation in resistant lines, particularly at 8 and 16 hpi, predominantly associated with ethylene and reactive oxygen species-mediated defense pathways. Moreover, DE transposons were predominantly up-regulated after inoculation and enriched near genes in Colfax. A long non-coding RNA (lncRNA) within the mapped region of the resistance gene exhibited exclusive up-regulation in the resistant lines after inoculation, potentially regulating two flanking LURP-one-related genes. Furthermore, DNA methylation analysis revealed increased CHH methylation levels in lncRNAs after inoculation, with delayed responses in Colfax compared to Williams 82. Overall, our results provide comprehensive insights into soybean responses to P. sansomeana, highlighting potential roles of lncRNAs and epigenetic regulation in plant defense.

plant biology↗

bioRxiv2024

Acceleration of HDL-mediated cellular cholesterol efflux alleviates periodontitis

Periodontitis (PD) is a common inflammatory disease known to be closely associated with metabolic disorders, particularly hyperlipidemia. However, direct evidence is lacking, and the molecular mechanism is yet to be examined. In the current study, we demonstrated that hypercholesterolemia is a causative factor in the development of PD. Logistic regression analysis revealed a strong positive correlation between PD and dyslipidemia. Data from in vivo (PD mouse model subjected to a high cholesterol diet) and in vitro (cholesterol treatment of periodontal cells) experiments showed that excess cholesterol influx into periodontal cells potentially contributes to periodontal inflammation and subsequently, alveolar bone erosion. Additionally, we compared the protective efficacies of cholesterol-lowering drugs with their different modes of action against PD pathogenesis in mice. Among the cholesterol-lowering drugs we tested, fenofibrate exerted the most protective effect against PD pathogenesis, due to an increased level of high-density lipoprotein cholesterol, a lipoprotein involved in cholesterol efflux from cells and reverse cholesterol transport. Indeed, cholesterol efflux was suppressed during PD progression by downregulation of the apoA-I binding protein (APOA1BP) expression in inflamed gingival fibroblasts and periodontal ligament cells. We also demonstrated that the overexpression of APOA1BP efficiently regulated periodontal inflammation and the subsequent alveolar bone loss by inducing cholesterol efflux. Our collective findings highlight the potential utility of currently available cholesterol-lowering medications for the mitigation of PD pathogenesis. By targeting the acceleration of high-density lipoprotein (HDL)-mediated cellular cholesterol efflux, a new therapeutic approach for PD may become possible.

cell biology↗

bioRxiv2023

Aberrant splicing in Huntington's disease via disrupted TDP-43 activity accompanied by altered m6A RNA modification.

Huntingtons disease (HD) is a neurodegenerative disorder caused by a CAG repeat expansion in the first exon of the HTT gene encoding huntingtin. Prior reports have established a correlation between CAG expanded HTT and altered gene expression. However, the mechanisms leading to disruption of RNA processing in HD remain unclear. Here, our analysis of the reported HTT protein interactome identifies interactions with known RNA-binding proteins (RBPs). Total, long-read sequencing and targeted RASL-seq of RNAs from cortex and striatum of the HD mouse model R6/2 reveals increased exon skipping which is confirmed in Q150 and Q175 knock-in mice and in HD human brain. We identify the RBP TDP-43 and the N6-methyladenosine (m6A) writer protein methyltransferase 3 (METTL3) to be upstream regulators of exon skipping in HD. Along with this novel mechanistic insight, we observe decreased nuclear localization of TDP-43 and cytoplasmic accumulation of phosphorylated TDP-43 in HD mice and human brain. In addition, TDP-43 co-localizes with HTT in human HD brain forming novel nuclear aggregate-like bodies distinct from mutant HTT inclusions or previously observed TDP-43 pathologies. Binding of TDP-43 onto RNAs encoding HD-associated differentially expressed and aberrantly spliced genes is decreased. Finally, m6A RNA modification is reduced on RNAs abnormally expressed in striatum from HD R6/2 mouse brain, including at clustered sites adjacent to TDP-43 binding sites. Our evidence supports TDP-43 loss of function coupled with altered m6A modification as a novel mechanism underlying alternative splicing/unannotated exon usage in HD and highlights the critical nature of TDP-43 function across multiple neurodegenerative diseases.

neuroscience↗

bioRxiv2023

Identification and neuroprotective properties of NA-184, a selective calpain-2 inhibitor

Our laboratory has shown that calpain-2 activation in the brain following acute injury is directly related to neuronal damage and the long-term functional consequences of the injury, while calpain-1 activation is generally neuroprotective and calpain-1 deletion exacerbates neuronal injury. We have also shown that a relatively selective calpain-2 inhibitor, referred to as C2I, enhanced long-term potentiation and learning and memory, and provided neuroprotection in the controlled cortical impact (CCI) model of traumatic brain injury (TBI) in mice. Similar results were also obtained in conditional calpain-2 knock-out mice. Using molecular dynamic simulation and Site Identification by Ligand Competitive Saturation (SILCS) software, we report here the discovery of a selective calpain-2 inhibitor NA-184, (S)-2-(3-benzylureido)-N-((R,S)-1-((3-chloro-2-methoxybenzyl)amino)-1,2-dioxopentan-3-yl)-4-methylpentanamide whose properties make it a good clinical candidate for the treatment of TBI.

neuroscience↗

bioRxiv2023

MurSS: Multi-resolution Selective Segmentation Model for Breast Cancer

We propose the Multi-resolution Selective Segmentation model (MurSS) for segmenting benign, Ductal Carcinoma In Situ, and Invasive Ductal Carcinoma in breast resection Hematoxylin and Eosin stained Whole Slide Images. MurSS simultaneously trains on context information from a wide area at low resolution and content information from a local area at high resolution, aiming for a more accurate diagnosis. Additionally, through the selection stage, it provides solutions for ambiguous tissue regions. Our proposed MurSS achieves a mean Intersection of Union performance of 91.1%, which is at least 16.8% and at most 19.0% higher than well-known image segmentation models.

bioinformatics↗

bioRxiv2023

Engineered retrons generate genome-independent protein-binding DNA for cellular control

DNA-protein interactions are core components of myriad natural and synthetic gene networks. Despite the potential new design space, DNA-protein interactions remain underexploited in vivo due to challenges in controlling specific DNA segments, including protein-binding sequences, independently of the genome. Here we engineer retrons, prokaryotic retroelements, to intracellularly generate genome-independent programmable small DNA for sequence-specific protein-binding. Using reprogrammed retron-derived DNA for allosteric transcription factor, we demonstrated dynamic regulation of synthetic gene networks and construction of automated feedback circuits for signal amplification, adaptation, and memory. Furthermore, we developed a new class of stimuli-responsive molecular "bait and prey" that enable modular, rapid, and post-translational control of protein subcellular localization. This work substantially expands possible application area of DNA-protein interactions, laying the foundation for technical advances in synthetic biology. One-Sentence SummaryWe demonstrate new ways to control, design, and exploit DNA-protein interactions in living cells using engineered retron-generated small DNA.

synthetic biology↗

bioRxiv2023

Validation of Dual Energy X-ray Absorptiometry for longitudinal quantification of tumor burden in a murine model of pancreatic ductal adenocarcinoma

Noninvasive imaging is central to preclinical, in vivo models of pancreatic ductal adenocarcinoma (PDAC). While bioluminescent imaging (BLI) is a gold standard, its signal is dependent on the metabolic activity of tumor cells. In contrast, dual energy X-ray absorptiometry (DEXA) is a direct measure of body composition. Thus, we aimed to assess its potential for longitudinal quantification of tumor burden versus BLI. We utilized the KCKO murine model of PDAC and subjected tumor-bearing (n = 20) and non-tumor control (NTC) (n = 10) animals to weekly BLI and DEXA measurements for up to 10 weeks. While BLI detected tumors at 1-week, it failed to detect tumor growth, displayed a decreasing trend overtime (slope = -9.0x108; p = 0.0028), and terminal signal did not correlate with ex vivo tumor mass (r = 0.01853; p = 0.6286). In contrast, DEXA did not detect elevated changes in abdominal cavity lean mass until week 2 post inoculation and tumors were not visible until week 3, but successfully quantified a tumor growth trend (slope = 0.7322; p<0.0001), and strongly correlated with final tumor mass (r = 0.9351; p<0.0001). These findings support the use of BLI for initial tumor engraftment and persistence but demonstrate the superiority of DEXA for longitudinal tumor burden studies. As tumor detection by DEXA is not restricted to luciferase expressing models, future studies to assess its value in various cancer models and as an in vivo outcome measure of treatment efficacy are warranted.

cancer biology↗

bioRxiv2023

A large effect genetic trade-off is caused by a single mutation in CBF2

Identifying the genetic basis of local adaptation and fitness trade-offs across environments is a central goal of evolutionary biology. Cold acclimation is an adaptive plastic response for surviving seasonal freezing, and costs of acclimation may be a general mechanism for fitness trade-offs across environments in temperate zone species. Starting with locally adapted ecotypes of Arabidopsis thaliana from Italy and Sweden, we examined the fitness consequences of a naturally occurring functional polymorphism in CBF2. This gene encodes a transcription factor that is a major regulator of cold-acclimated freezing tolerance, and resides within a locus responsible for a genetic trade-off for long-term mean fitness. We estimated the consequences of alternate genotypes of CBF2 on 5-year mean fitness and fitness components at the native field sites by comparing near isogenic lines with alternate genotypes of CBF2 to their genetic background ecotypes. The effects of CBF2 were validated at the nucleotide level using gene edited lines in the native genetic backgrounds grown in simulated parental environments. The foreign CBF2 genotype in the local genetic background reduced long-term mean fitness in Sweden by more than 10%, primarily via effects on survival. In Italy, fitness was reduced by more than 20%, primarily via effects on fecundity. At both sites, the effects were temporally variable and much stronger in some years. The gene edited lines confirmed that CBF2 encodes the causal variant underlying this genetic trade-off. Additionally, we demonstrated a substantial fitness cost of cold acclimation, which has broad implications for potential maladaptive responses to climate change.

evolutionary biology↗

bioRxiv2023

De novo production of an antitumor precursor actinocin and other medicinal molecules from kynurenine pathway in Escherichia coli

Kynurenine pathway has a potential to convert L-tryptophan into multiple medicinal molecules. This study aims to explore the biosynthetic potential of kynurenine pathway for the efficient production of actinocin, an antitumor precursor selected as a proof-of-concept target molecule. Kynurenine pathway is first constructed in Escherichia coli by testing various combinations of biosynthetic genes from four different organisms. Metabolic engineering strategies are next performed to improve the production by inhibiting a competing pathway, and enhancing intracellular supply of a cofactor S-adenosyl-L-methionine, and ultimately to produce actinocin from glucose. Metabolome analysis further suggests additional gene overexpression targets, which finally leads to the actinocin titer of 719 mg/L. E. coli strain engineered to produce actinocin is further successfully utilized to produce 350 mg/L of kynurenic acid, a neuroprotectant, and 1401 mg/L of 3-hydroxyanthranilic acid, an antioxidant, also from glucose. These competitive production titers demonstrate the biosynthetic potential of kynurenine pathway as a source of multiple medicinal molecules. The approach undertaken in this study can be useful for producing other molecules associated with kynurenine pathway.

synthetic biology↗

bioRxiv2023

Prediction of metabolites associated with somatic mutations in cancers by using genome-scale metabolic models and mutation data

BackgroundOncometabolites, often generated as a result of a gene mutation, show pro-oncogenic function when abnormally accumulated in cancer cells. Identification of such mutation-associated metabolites will facilitate developing treatment strategies for cancers, but is challenging due to a large number of metabolites in a cell and the presence of multiple genes associated with cancer development. ResultsHere we report the development of a computational workflow that predicts metabolite-gene-pathway sets (MGPs). MGPs present metabolites and metabolic pathways significantly associated with specific somatic mutations in cancers. The computational workflow uses both cancer patient-specific genome-scale metabolic models (GEMs) and mutation data to generate MGPs. A GEM is a computational model that predicts reaction fluxes at a genome scale, and can be constructed in a cell-specific manner by using omics data (e.g., RNA-seq). The computational workflow is first validated by comparing the resulting metabolite-gene (MG) pairs with multi-omics data (i.e., mutation data, RNA-seq data, and metabolome data) from 17 acute myeloid leukemia samples and 21 renal cell carcinoma samples collected in this study. The computational workflow is further validated by evaluating the MGPs predicted for 18 cancer types, by using RNA-seq data publicly available, in comparison with the reported studies. Therapeutic potential of the resulting MGPs is also discussed. ConclusionsValidation of the MGP-predicting computational workflow indicates that a decent number of metabolites and metabolic pathways appear to be significantly associated with specific somatic mutations. The computational workflow and the resulting MGPs will help identify novel oncometabolites, and also suggest cancer treatment strategies.

systems biology↗

bioRxiv2023

Distinct phases of cellular signaling revealed by time-resolved protein synthesis

The post-translational regulation of protein function is involved in most cellular processes. As such, synthetic biology tools that operate at this level provide opportunities for manipulating cellular states. Here, we deploy a proximity-triggered protein trans-splicing technology to enable the time-resolved synthesis of target proteins from pre-made parts. The modularity of the strategy allows for the addition or removal of various control elements as a function of the splicing reaction, in the process permitting the cellular location and/or activity state of starting materials and products to be differentiated. The approach is applied to a diverse set of proteins, including the kinase oncofusions BCR/ABL and DNAJB1/PRKACA where dynamic cellular phosphorylation events are dissected, revealing distinct phases of signaling and identifying molecular players connecting the oncofusion to cancer transformation as novel therapeutic targets of cancer cells. We envision that the tools and control strategies developed herein will allow the activity of both naturally occurring and designer proteins to be harnessed for basic and applied research.

biochemistry↗

bioRxiv2023

The super-healing MRL strain promotes muscle growth in muscular dystrophy through a regenerative extracellular matrix

Genetic background shifts the severity of muscular dystrophy. In mice, the DBA/2J strain confers a more severe muscular dystrophy phenotype, whereas the Murphys Roth Large (MRL) strain has "super-healing" properties that reduce fibrosis. A comparative analysis of the Sgcg null model of Limb Girdle Muscular Dystrophy in the DBA/2J versus MRL strain showed the MRL background was associated with greater myofiber regeneration and reduced structural degradation of muscle. Transcriptomic profiling of dystrophic muscle in the DBA/2J and MRL strains indicated strain-dependent expression of the extracellular matrix (ECM) and TGF-{beta} signaling genes. To investigate the MRL ECM, cellular components were removed from dystrophic muscle sections to generate decellularized "myoscaffolds". Decellularized myoscaffolds from dystrophic mice in the protective MRL strain had significantly less deposition of collagen and matrix-bound TGF-{beta}1 and TGF-{beta}3 throughout the matrix, and dystrophic myoscaffolds from the MRL background were enriched in myokines. C2C12 myoblasts were seeded onto decellularized matrices from Sgcg-/- MRL and Sgcg-/- DBA/2J matrices. Acellular myoscaffolds from the dystrophic MRL background induced myoblast differentiation and growth compared to dystrophic myoscaffolds from the DBA/2J matrices. These studies establish that the MRL background also generates its effect through a highly regenerative ECM, which is active even in muscular dystrophy. Brief SummaryThe extracellular matrix of the super-healing MRL mouse strain harbors regenerative myokines that improve skeletal muscle growth and function in muscular dystrophy. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=120 SRC="FIGDIR/small/547098v1_ufig1.gif" ALT="Figure 1"> View larger version (49K): org.highwire.dtl.DTLVardef@18543eborg.highwire.dtl.DTLVardef@2e3386org.highwire.dtl.DTLVardef@138d5ccorg.highwire.dtl.DTLVardef@5c4ef6_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗

bioRxiv2023

Serine synthesis pathway upregulated by E-cadherin is essential for the proliferation and metastasis of breast cancers

The loss of E-cadherin (E-cad), an epithelial cell adhesion molecule, has been implicated in the epithelial-mesenchymal transition (EMT), promoting invasion and migration of cancer cells and, consequently, metastasis. However, recent studies have demonstrated that E-cad supports the survival and proliferation of metastatic cancer cells, suggesting that our understanding of E-cad in metastasis is far from comprehensive. Here, we report that E-cad upregulates the de novo serine synthesis pathway (SSP) in breast cancer cells. The SSP provides metabolic precursors for biosynthesis and resistance to oxidative stress, critically beneficial for E-cad-positive breast cancer cells to achieve faster tumor growth and more metastases. Inhibition of PHGDH, a rate-limiting enzyme in the SSP, significantly and specifically hampered the proliferation of E-cad-positive breast cancer cells and rendered them vulnerable to oxidative stress, inhibiting their metastatic potential. Our findings reveal that E-cad adhesion molecule significantly reprograms cellular metabolism, promoting tumor growth and metastasis of breast cancers.

cancer biology↗