Biology subjects

Maeda, Y.

Publications and source records attributed to Maeda, Y..

At least 19 recordsLinked to original sources

bioRxiv2026

Biosynthesis of prenylated flavonoids by two membrane-bound prenyltransferases in glandular trichomes of Macaranga tanarius.

Macaranga tanarius (Euphorbiaceae), a myrmecophilic plant grown in subtropical countries, was identified as a source of Okinawan propolis, a honeybee product, which is glandular trichomes developed on the surface of the fruits. This tissue contains a high amount of characteristic geranylated flavonoids known as nymphaeols (nymphaeol A - C and isonymphaeol B), which exhibit strong antioxidant activity. In this study, we characterized the structure of glandular trichomes of M. tanarius, showing that they are sac-like structures containing drupelet-like aggregates of secretary cells, and a subcuticular cavity was also observed. From a cDNA library, we identified two prenyltransferase (PT) genes involved in biosynthesis of nymphaeols, and a PT gene grouped in a primary metabolic PT. Our biochemical experiments demonstrated that one of the former secondary metabolic PTs (MtPT1) is a B-ring-specific geranyltransferase for eriodictyol to yield nymphaeols B and isonymphaeol B. MtPT1 was unusual for a plant PT, an enzyme that yielded multiple reaction products. The other PT (MtPT3) transferred a geranyl moiety to the A-ring of eriodictyol to form nymphaeol A. Although dimethylallyl diphosphate (DMAPP) was not recognized as its prenyl donor substrate of eriodictyol, giving a B-ring geranylated eriodyctiol as the prenyl acceptor substrate, this enzyme used DMAPP to attach the prenyl moiety to the A-ring and produced nymphaeol C. These data suggest that M. tanarius has evolved its PT function to produce a diverse range of prenylated flavonoids using a limited set of genes.

biochemistry↗

bioRxiv2026

A novel recombinant BCG vaccine using a mycobacteriophage promoter shows improved protection against tuberculosis

The limited efficacy of conventional bacillus Calmette-Guerin (BCG) vaccination against adult pulmonary tuberculosis highlights the need for improved vaccine strategies. Genome integration can overcome the plasmid instability of recombinant BCG, but we hypothesized that this approach would be constrained by reduced transcriptional activity of conventional promoters when present as a single genomic copy. Here we identified P79, a mycobacteriophage-derived promoter that sustains high-level expression from a single genomic locus and used it to construct a genome-integrated recombinant BCG, termed LRC-BCG. LRC-BCG secretes the HSP70-MMPII fusion antigen flanked by the PEST sequences, maintained stable antigen expression over serial passages, and induced strong activation of macrophages and dendritic cells in vitro. In vivo, LRC-BCG inhibited Mycobacterium tuberculosis multiplication more effectively than conventional BCG, even at low doses. These findings demonstrate the feasibility of using P79 for stable genome-integrated recombinant BCG and support LRC-BCG as a promising tuberculosis vaccine candidate.

microbiology↗

bioRxiv2026

Transposon insertion sequencing identifies genetic determinants of intrinsic rifamycin resistance in Mycobacterium abscessus

Mycobacterium abscessus exhibits intrinsic resistance to many antimicrobial agents, including rifampicin, a frontline anti-tuberculosis drug, severely limiting treatment options. Here, we used transposon insertion sequencing (Tn-Seq) to perform a genomewide screen to identify genes required for intrinsic rifampicin resistance in M. abscessus. We uncovered candidate genes that confer intrinsic resistance to the rifamycin-class antibiotics, rifampicin and rifabutin. The genes we identified included previously reported genes such as arr, helR, and MAB_2807. By comparing our results with the rifampicin intrinsic resistance gene in Mycobacterium tuberculosis, we found that the mechanisms underlying rifampicin intrinsic resistance were distinct between the two species. The contribution of seven representative candidate genes to rifampicin resistance was confirmed by characterizing targeted gene deletion or transposon insertion mutants. Among these determinants, MAB_2807 was identified as a major efflux-based contributor to rifamycin resistance, and its disruption increased intracellular rifampicin accumulation. In addition to known resistance determinants, Tn-Seq revealed contributions from many genes involved in cell envelope processes to rifamycin resistance. Guided by this genetic signature, we evaluated the combined effects of cell wall-targeting antimicrobial agents with rifamycins. We found that rifamycins displayed selective synergistic interactions with specific {beta}-lactam antibiotics. Interestingly, we found that rifamycin exposure altered cell envelope ultrastructure and increased the accumulation of the peptidoglycan precursor UDP-N-acetylglucosamine, suggesting that rifampicin perturbs envelope-associated metabolic homeostasis. These findings highlight rifamycin-induced vulnerable cellular processes that may inform rational combination strategies. ImportanceRifamycins are cornerstone antibiotics for the treatment of mycobacterial infections, yet they are ineffective against Mycobacterium abscessus. Although several key resistance mechanisms have been described, the full genetic basis of intrinsic rifamycin resistance remains to be elucidated. Here, we used transposon insertion sequencing to systematically identify genes that contribute to intrinsic rifamycin resistance in M. abscessus. Because recent studies have shown that chemical modification of rifamycins can overcome specific intrinsic resistance mechanisms, a comprehensive understanding of these determinants could facilitate the development of next-generation rifamycins with improved activity against M. abscessus. In addition, we unexpectedly found that rifamycin exposure alters cell envelope structure, the intracellular levels of a key metabolic intermediate in peptidoglycan biosynthesis, and susceptibility to certain {beta}-lactams in M. abscessus. These findings may help guide the rational development of combination therapeutic strategies with next-generation rifamycins.

microbiology↗

bioRxiv2026

HIV-1 can undergo Env-independent retrotransposon-like activity

Retrovirus replication requires coordinated interplay between viral proteins and host cellular machinery, including reverse transcription of the viral RNA genome into DNA and its subsequent integration into the host genomes. SOX2-dependent retrotransposon dynamics have been reported for endogenous retrovirus HERV-K; however, whether a similar intracellular pathway exists for exogenous retroviruses remains unclear. To address whether infection-independent intracellular reverse transcription and partial integration can occur, that is, whether retrovirus can exhibit retrotransposon-like activity, we utilized HeLa and 293T cells, which express no HIV-1 entry receptors. We engineered an Env-deficient HIV-1 NL4-3-based reporter encoding a reverse-oriented, intron-disrupted nanoluciferase cassette that becomes expressible only after splicing followed by reverse transcription. We found that reporter activation depends on reverse transcriptase and protease activities. While integrase is dispensable for early expression, it is essential for long-term maintenance of the nanoluciferase signal. Integration site mapping using next-generation sequencing further confirmed that stable reporter activity requires integrase-dependent proviral insertion. Functional analysis of Gag revealed that membrane binding, multimerization, and budding are prerequisite steps for reporter activation. Concentrated virus preparations from culture supernatants failed to activate the reporter in 293T cells, ruling out a role for reinfection. Electron and confocal microscopy suggested that Gag or viral particles traffic through endosomal compartments. Furthermore, inhibition of dynamin- and clathrin-dependent endocytic pathways reduced reporter activity, indicating that these pathways contribute to efficient reporter activity. Collectively, these finding support the conclusion that HIV-1 can undergo intracellular reverse transcription and partial integration in an infection-independent manner, prompting a reconsideration of the boundary between exogenous retroviruses and endogenous retroelements. Author summaryEnv-independent, infection-independent intracellular reverse transcription and integration in HIV-1 may contribute to integration-site diversity within the same cell. More broadly, this phenomenon suggests continuity between the retroviral life cycle and retrotransposition dynamics, therefore informing our understanding of host-virus coevolution, mechanisms of long-term persistence, and the redesign of therapeutic strategies targeting pre-integration steps.

microbiology↗

bioRxiv2025

M-Sec promotes the production of infectious HIV-1 virus through the exocyst complex

We have demonstrated that the cellular protein M-Sec promotes the transmission of human immunodeficiency virus type 1 (HIV-1). However, the underlying mechanism is not fully understood. Here, we report that M-Sec promotes the production of infectious HIV-1 virus. The major viral structural protein Gag distributed as many puncta in infected cells, which is one of the indicators of viral particle formation. The knockdown of M-Sec hindered the Gag puncta formation and co-localization of Gag with the viral envelope protein Env in cells, and reduced the amount of Env and infectivity of the produced virus. Consistent with these results, the over-expression of M-Sec induced the accumulation of Gag puncta, Gag/Env co-localization, and Env incorporation into virus and viral infectivity. M-Sec is known to bind phosphatidylinositol 4,5-bisphosphate (PIP2) and a small GTPase Ral, both of which were required for the M-Sec-mediated HIV-1 regulation. The exocyst complex, which is the downstream effector of Ral, was also required for the M-Sec-mediated HIV-1 regulation. Because PIP2, Ral and the exocyst complex are important for the M-Sec-mediated formation of the long plasma membrane protrusions, the present study suggests that M-Sec promotes HIV-1 transmission by acting on both cell structures and viral production through these overlapping components. Author SummaryDespite an effective anti-retroviral therapy, human immunodeficiency virus type 1 (HIV-1) persists in a fraction of infected cells, which is an obstacle to cure. HIV-1 exploits the cell-to-cell infection for its transmission, which is more efficient than infection by cell-free virus. Thus, it is important to fully understand the process of cell-to-cell infection towards the HIV-1 cure. We previously identified M-Sec as the cellular protein that potentiates the cell-to-cell infection of HIV-1. However, the underlying mechanism is not fully explained. In this study, we discovered that M-Sec promotes the production of infectious HIV-1 particles. Mechanistically, M-Sec affects the intracellular dynamics of the major viral structural protein Gag, which leads to an efficient incorporation of the viral envelope protein Env into viral particles. This activity of M-Sec depends on PIP2 (the phosphoinositide), Ral (the small GTPase), and the exocyst complex (the downstream effector of Ral), all of which are involved in vesicular trafficking. Thus, the present study identifies M-Sec and related molecular components as potential targets of anti-HIV-1 strategies.

microbiology↗

bioRxiv2025

Artificial Intelligence-driven Whole-brain Cell Mapping with Highly Multiplexed In Situ Hybridization

Recent advances in three-dimensional single-cell-resolution imaging have begun to link organ-wide and cellular level research in development and disease research. Harnessing the power of whole-mount cell staining and tissue-clearing, it became possible to quantify the cell populations throughout an intact organ. While powerful, whole-organ imaging remains limited by the inability to stain a broad range of molecular markers simultaneously and by the lack of an analytical scheme to precisely quantify the cell population. Here, we present a highly multiplexed whole-mount staining technique, utilizing the repeated application of fluorescent in situ hybridization. This technique, termed mFISH3D, was designed by extensively dissecting the chemical basis of hybridization reactions in fixed tissue. mFISH3D enabled the visualization of 10 types of mRNAs in an intact mouse brain and has been demonstrated in various biological specimens including the human brain. To achieve unprecedented levels of accuracy in spatial cell mapping, we developed artificial intelligence (AI)-driven workflow using self-supervised learning, significantly reducing the need for extensive manual annotations. The integration of mFISH3D with our AI solution sets a standard for high-dimensional tissue analysis, provides a new systematic framework for analyzing complex cellular ecosystems and enables comprehensive investigation of selective cellular vulnerabilities in diseases.

neuroscience↗

bioRxiv2025

High-Throughput Measurement of Oxidative Stress Indicators: d-ROMs and BAP Assays in a 384-Well Plate Format

The bodys oxidative balance is regulated by systems that produce and eliminate reactive oxygen species (ROS), and disruptions in this balance can contribute to the development of lifestyle-related diseases. d-ROMs and BAP tests, which evaluate oxidative balance using just 30 {micro}L of serum per sample in approximately 10 minutes, are widely used for this purpose. However, these methods are not suitable for large-scale studies due to their low-throughput and cost. To overcome these limitations, we established a simultaneous measurement system for multiple samples (144 samples) for measuring d-ROMs and BAP using a pipetting robot and a 384-well plate. The developed system demonstrated good linearity and reproducibility, while significantly reducing reagent and sample consumption. Measurement differences compared to the one of the currently available FREE Carrio Duo system ranged from -5% to 3% for d-ROMs and -12% to 8% for BAP, indicating high consistency with existing methods. Furthermore, the measurement time was substantially shortened from 24 hours (10 minutes x 144 samples) to at longest four hours, although the final color measurements for d-ROMs were performed one week later. This optimized semi-automated system enables the precise and efficient measurement of oxidative stress markers, making it suitable for large-scale studies.

biochemistry↗

bioRxiv2025

Lenacapavir binding to immature Gag triggers the emergence of giant HIV-1 virions

Lenacapavir (LEN), a potent capsid inhibitor, suppresses reverse transcription and nuclear import by disrupting capsid core formation in human immunodeficiency virus type 1 (HIV-1). However, its effect on the late-stage viral assembly remains unclear. Although p24 ELISA suggested that LEN inhibited HIV-1, both RT-dPCR and Vpr-HiBiT assays indicated no reduction in the viral output. This discrepancy was attributed to LEN-induced epitope masking of p24, which was reversed by altered sample processing. Furthermore, LEN induced numerous abnormal, discrete clusters of Gag at the plasma membrane. Mass photometry and transmission electron microscopy revealed heterogeneous viral-like particles (LENiVLPs; diameter >200 nm), containing both Gag and Env proteins. Although LENiVLPs retained membrane fusion capability, they were non-infectious owing to post-entry defects. Thus, LEN binds to the precursor Gag and promotes aberrant particle formation, offering novel insights that could guide the development of next-generation LEN-based therapeutics targeting the late stages of the viral life cycle.

microbiology↗

bioRxiv2025

Systemic aldehyde storm induced by allyl alcohol exposure results in extensive hepatic ferroptosis in Aldh2*2 knock-in mice

Aldehyde dehydrogenase 2 (ALDH2) is a mitochondrial enzyme that detoxifies multiple aldehyde species in the body. The ALDH2*2 allele (E487K) is one of the most common gene polymorphisms in humans, resulting in dysfunction of its enzyme activity. This study investigated in vivo mechanism of acute liver injury caused by exposure to allyl alcohol (AA) using Aldh2*2 knock-in (KI) mice with the same amino acid replacement as human ALDH2*2. A rapid burst of plasma acrolein as an active metabolite of AA, as well as plasma endogenous reactive aldehydes malondialdehyde (MDA) and formaldehyde, was observed at 10 min after exposure to 75 mg/kg of AA in the Aldh2*2 KI homozygous mice, which was not evident in the wild-type mice. Hepatocellular necrosis was more extensive in the Aldh2*2 KI homozygous mice than in the wild-type mice, which was preceded by hepatic glutathione depletion and was coincident with an accumulation of acrolein, MDA, and 4-hydroxy-2-nonenal adducts and iron deposition, suggesting an involvement of ferroptosis in the exacerbation of hepatic necrosis. Recovery from hepatic glutathione depletion was delayed in the homozygous mice compared with the wild-type mice, with a decreasing tendency of hepatic expression of cystine transporter xCT. These results suggest that increased hepatic glutathione consumption, due to decreased aldehyde detoxification capacity, can sensitize the Aldh2*2 KI homozygous mice to hepatic ferroptosis after the rapid "aldehyde storm". Our study revealed a crosstalk between aldehyde metabolism and ferroptosis pathways and potential health impacts of endogenous reactive aldehydes on ALDH2*2 carriers.

pathology↗

bioRxiv2025

HNF4α controls growth, identity and response to KRAS inhibition of invasive mucinous adenocarcinoma of the lung

Cellular plasticity is a hallmark of cancer, enabling tumor cells to alter identity and evade therapeutic pressure. In invasive mucinous adenocarcinoma of the lung (IMA), NKX2-1 loss triggers a pulmonary to gastric switch marked by aberrant activation of HNF4, a master regulator of gastrointestinal/hepatic differentiation. We find that HNF4 promotes IMA growth and activates a gastric pit cell-like program. Hnf4a deletion induces IMA dedifferentiation, enabling FoxA1/2 to access de novo sites and activate alternative identities. HNF4 also induces a mucinous program associated with tolerance to KRAS blockade, and HNF4 loss enhances response to KRASG12D inhibition. Mechanistically, HNF4 blocks cell cycle exit in drug-tolerant persister cells and promotes activity of the antioxidant transcription factor NRF2. NRF2 activation partially rescues effects of Hnf4a deletion on KRASG12D inhibition, whereas NRF2 inhibition enhances sensitivity to KRASG12D blockade. Thus, HNF4 is a key regulator of identity and primary response to KRASG12D inhibition in IMA. SIGNIFICANCEIMA is a genetically and epigenetically distinct LUAD subtype for which targeted therapies are lacking due to the high proportion of KRAS mutations. This study points to blockade of the HNF4 -> NRF2 axis as a potential strategy to enhance primary response to KRAS inhibition in IMA.

cancer biology↗

bioRxiv2025

Mucosal innate immune activation as the trigger to Prevotella species-induced arthritis in genetically resistant mice

An altered gut microbiota, particularly the expansion of Prevotellaceae members, is increasingly implicated in the pathogenesis of rheumatoid arthritis (RA), yet the mechanisms hind this phenomenon remain unclear. Here, we demonstrate that Palleniella intestinalis, a member of the Prevotellaceae family, induces a 100% arthritis incidence in genetically resistant C57BL/6 mice. Inoculation with P. intestinalis modifies gut microbiota ecology, increases intestinal permeability, and selectively activates colonic CD11bCD11c myeloid cells, facilitating Th17 differentiation and driving joint inflammation. In vitro, outer membrane vesicles (OMV) from P. intestinalis and Segatella copri (formerly known as Prevotella copri) prime bone marrow-derived dendritic cells (BMDCs) to drive Th17 differentiation in an IL-6-dependent manner. Similar changes with increase in innate immune cell activation and IL-6 levels were shown in gut biopsies from new-onset RA patients. The transfer of Prevotellaceae-derived OMVs or Prevotellaeae-primed BMDCs replicates the hightened arthritis incidence in resistant mice, highlighting the critical role of intestinal immune activation in RA. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=130 SRC="FIGDIR/small/643707v1_ufig1.gif" ALT="Figure 1"> View larger version (36K): org.highwire.dtl.DTLVardef@1ce227corg.highwire.dtl.DTLVardef@3a2d0eorg.highwire.dtl.DTLVardef@16404b6org.highwire.dtl.DTLVardef@1717dc1_HPS_FORMAT_FIGEXP M_FIG C_FIG O_LIColonization with Paleniella intestinalis bypasses genetic resistance, consistently inducing arthritis incidence in non-susceptible C57BL/6 mice C_LIO_LIP. intestinalis activates colonic CD11b+CD11c+ myeloid cells, driving systemic Th17 cell differentiation C_LIO_LIIn vitro, outer membrane vesicles from P. intestinalis or RA-derived S. copri RPC01 primed DCs that drive Th17 differentiation in an IL-6-dependent manner C_LIO_LITransfer of P. intestinalis-primed DCs or its outer membrane vesicles alone increases arthritis incidence in non-susceptible C57BL/6 mice C_LI

immunology↗

bioRxiv2025

Open-source Photobleacher for Fluorescent Imaging of Large Pigment-Rich Tissues

Fluorescent imaging enables visualization of the specific molecules of interest with high contrast, and the use of multiple fluorophores in a single tissue sample allows visualization of complex relationships between biological molecules, cell types, and anatomy. The utility of fluorescent imaging in human tissue has been limited by endogenous pigments that can block the light path or emit an autofluorescence, thereby interfering with the specific imaging of target molecules. Although photobleachers have been developed to quench endogenous pigments, the lack of customizability limits their utility for a broad range of applications. Here, we present a high luminous-intensity photobleacher that is based on rigorous simulations of illumination patterns using the laws of radiation, along with the framework to maximize bleaching efficiency. This open-source project is designed to help researchers customize and scale according to the tissue types and the research goals. The photobleacher is applicable to both thin tissue slices and large-volume cleared tissue samples to enable serial three-dimensional imaging of postmortem human brain using multiplexed antibody or oligonucleotide probes. SIGNIFICANCE STATEMENTPhotobleaching is an effective technique for quenching endogenous pigments, enabling multiplexed fluorescent imaging of pigment-rich tissues, such as postmortem human samples. While many photobleaching strategies have been proposed, there is no standard guidance on how to design and use a photobleacher. This study introduces a general strategy for designing an effective, scalable, and customizable photobleacher, and proposes a workflow for properly treating tissues with the photobleacher. The technique enables high-contrast molecular visualization in tissues of various sizes, including large volumetric cleared tissues. Our framework will accelerate the quantitative understanding of human molecular anatomy and is applicable to diverse biological fields, including medical diagnostics.

neuroscience↗

bioRxiv2025

Microscopic and structural observations of actin filament capping and severing by Cytochalasin D

Cytochalasin D (CytoD) is widely used to inhibit actin polymerization, but the underlying regulatory mechanism is unclear. We addressed this using Total Internal Reflection Fluorescence (TIRF) microscopy. Our time course depolymerization assay of individual actin filaments showed that CytoD tightly caps the barbed end, with an estimated Km value for inhibition of 4.1 nM and a duration time of [~]1 min. Consistently, in polymerization assays, CytoD at concentrations near the Km value completely suppressed barbed end elongation. Interestingly, at lower concentrations, CytoD acted as a leaky capper, allowing actin monomer addition by rapidly binding to and dissociating from barbed ends. We interpreted this contradictory behavior as arising from differences in binding modes: capping one strand (fast dissociation) or both strands (slow dissociation). CytoD severs actin filaments at micromolar levels, a concentration range commonly used in cell biological studies. Although the severing rate is slower than cofilin, the frequency is higher, resulting in the fragmentation of filaments into shorter pieces. Severing activity was suppressed by inorganic phosphate or cofilin. We determined the crystal structure of CytoD bound to filamentous conformation (F-form) actin and found that CytoD fits better in the hydrophobic cleft of F-form actin than in the monomeric conformation actin, explaining the preferential binding towards barbed end subunits. The structure further indicates that CytoD prevents barbed end depolymerization by stabilizing the terminal subunits in the F-form, which is supported by our MD simulations. Collectively, our results demonstrate how CytoD regulates actin dynamics at the molecular level.

biophysics↗

bioRxiv2025

Impact of Low-Dose Narrowband UV Radiation on Skin Tissue and Mast Cells in a Canine Model

Narrowband ultraviolet radiation (NB-UVR) therapy is widely utilized in dermatology worldwide. While the immunosuppressive effects of ultraviolet radiation are well-documented, its non-inflammatory effects remain poorly understood. This study evaluated the effects of sub-minimal erythema dose (MED) narrowband ultraviolet radiation using a canine model. The effects of narrowband-ultraviolet B (310 nm) and A2 wavelengths (320 and 330 nm) were compared. Initially, we demonstrated the therapeutic potential of NB-UVR in dogs with spontaneous atopic dermatitis (n = 6, p < 0.05). Following 300 mJ/cm{superscript 2} sub-MED ultraviolet radiation exposure, intradermal skin testing, skin mast cell counts, and RNA sequencing analysis were conducted. Additionally, cell viability (WST assay) and apoptosis (DAPI staining) were assessed in vitro using a canine mast cell line. Ultraviolet radiation exposure significantly reduced intradermal skin test scores across all wavelengths and decreased skin mast cell counts at 310 nm (n = 3, p < 0.05). In vitro, cell viability was significantly reduced at 310 and 320 nm (p < 0.05), and 310 nm irradiation specifically increased apoptotic cell numbers (p < 0.05). RNA sequencing identified 71 differentially expressed genes at 320 nm, with enrichment analysis highlighting muscle cell components and functions, potentially associated with arrector pili muscle activity. These findings suggest that 310 nm irradiation induces apoptosis, while 320 nm elicits non-inflammatory modulatory effects, highlighting distinct wavelength-specific therapeutic mechanisms of narrowband ultraviolet radiation.

immunology↗

bioRxiv2024

In vivo transition in chromatin accessibility during differentiation of deep-layer excitatory neurons in the neocortex

During the differentiation process of neurons, their gene transcription pattern changes according to both intrinsic and extrinsic stimuli-induced programs. Chromatin regulation at regulatory elements is involved in this precise control of gene expression. However, developmental changes in chromatin accessibility of the cortical neurons in vivo are less understood, partly because there is no convenient method to genetically label neurons of a specific lineage. Here, we establish a method for labeling the differentiating neurons of specific birthdates. Using this method, we traced the four-day differentiation process of in vivo deep-layer excitatory neurons in mouse embryonic cortex and examined the changes in the genome-wide transcription pattern and chromatin accessibility with RNA-seq and DNase-seq, respectively. The genomic regions of genes associated with mature neuron functions, such as deep layer-specific genes and genes responsive to external stimuli, became open even in the embryonic stage. Moreover, genes with bivalent marks in neural precursor/stem cells (NPCs) became open. Together, our data demonstrate the importance of chromatin regulation in vivo differentiating neurons during the embryonic stage to follow activation of neuronal genes in their maturation process.

developmental biology↗

bioRxiv2024

PBAE-PEG based lipid nanoparticles for lung cell-specific gene delivery

Delivery of modified mRNA encapsulated in lipid nanoparticles, exemplified by their successful use in COVID-19 vaccination, provides a framework for treating various genetic and acquired disorders. Herein, we developed PEGylated(PBAE-PEG) and non-PEGylated(PBAE) PBAE with lipids 4A3-SC8/DOPE/cholesterol/DOTAP to form lipid nanoparticles (LNPs) for mRNA delivery into different types of pulmonary cells in vivo. PBAE-PEG/LNP were highly active in transfecting HEK293T cells and air-liquid interfaced H441 cells in vitro. PBAE-PEG/LNP were used to express Cre-recombinase after administration to mice by intravenous injection, resulting in high transfection levels in pulmonary vascular endothelial cells. Intratracheal injection of both PBAE-PEG/LNP and PBAE/LNPs resulted in efficient and selective transfection of lung epithelial cells, identified by the expression of stabilized Cre-recombinase mRNA in club cells and alveolar type 2 cells. PBAE-PEG/LNP were most effective in transfecting alveolar type 2 cells after intratracheal injection, while PBAE/LNPs administered intratracheally were more effective in transfecting secretory airway cells. Cre-mediated recombination was specific to lung epithelial cells after intratracheal administration. Likewise, intravenous administration resulted in selective transfection of endothelial cells but not other pulmonary cell types, indicating their failure to cross the pulmonary endothelial-to-epithelial barrier. Moreover, 5-methoxyuridine modified mRNA was more efficient than unmodified mRNA in vivo but not in vitro.

bioengineering↗

bioRxiv2024

Genome-wide mapping of autonomously replicating sequences in the marine diatom Phaeodactylum tricornutum

Autonomously replicating sequences (ARSs) are important accessories in episomal vectors that allow them to be replicated and stably maintained within transformants. Despite their importance, no information on ARSs in diatoms have been reported. Therefore, we attempted to identify ARS candidates in the model diatom, Phaeodactylum tricornutum, via chromatin immunoprecipitation sequencing. In this study, subunits of the origin recognition complex (ORC), ORC2 and ORC4, were used to screen for ARS candidates. ORC2 and ORC4 bound to 355 sites on the P. tricornutum genome, of which 69 were constantly screened after multiple attempts. The screened ARS candidates had an AT-richness of approximately 50% (44.39-52.92%) and did not have conserved sequences. In addition, ARS candidates were distributed randomly but had a dense distribution pattern at several sites. Their positions tended to overlap with those of the genetic region (73.91%). Compared to the ARSs of several other eukaryotic organisms, the characteristics of the screened ARS candidates are complex. Thus, our findings suggest that the diatom has a distinct and unique native ARSs.

molecular biology↗

bioRxiv2024

Patho-transcriptomic analysis of invasive mucinous adenocarcinoma of the lung (IMA): comparison with lung adenocarcinoma with signet ring cell features (SRCC)

BackgroundInvasive mucinous adenocarcinoma (IMA) comprises [~]5% of lung adenocarcinoma. There is no effective therapy for IMA when surgical resection is not possible. IMA is sometimes confused with adenocarcinoma with signet ring cell features (SRCC) pathologically since both adenocarcinomas feature tumor cells with abundant intracellular mucin. The molecular mechanisms by which such mucin-producing lung adenocarcinomas develop remain unknown. MethodsUsing a Visium spatial transcriptomics approach, we analyzed IMA and compared it with SRCC patho-transcriptomically. Combining spatial transcriptomics data with in vitro studies using RNA-seq and ChIP-seq, we assessed downstream targets of transcription factors HNF4A and SPDEF that are highly expressed in IMA and/or SRCC. ResultsSpatial transcriptomics analysis indicated that there are 6 distinct cell clusters in IMA and SRCC. Notably, two clusters (C1 and C3) of mucinous tumor cells exist in both adenocarcinomas albeit at a different ratio. Importantly, a portion of genes (e.g., NKX2-1, GKN1, HNF4A and FOXA3) are distinctly expressed while some mucous-related genes (e.g., SPDEF and FOXA2) are expressed in both adenocarcinomas. We determined that HNF4A induces MUC3A/B and TM4SF4 and that BI 6015, an HNF4A antagonist, suppressed the growth of IMA cells. Using mutant SPDEF that is associated with COVID-19, we also determined that an intact DNA-binding domain of SPDEF is required for SPDEF-mediated induction of mucin genes (MUC5AC, MUC5B and AGR2). Additionally, we found that XMU-MP-1, a SPDEF inhibitor, suppressed the growth of IMA cells. ConclusionThese results revealed that IMA and SRCC contain heterogenous tumor cell types, some of which are targetable.

cancer biology↗