Biology subjects

Hasegawa, Y.

Publications and source records attributed to Hasegawa, Y..

At least 19 recordsLinked to original sources

bioRxiv2026

The congruency between anger intensity and reddish facial color modulates the early posterior negativity (EPN)

Facial color is associated with the perceptual evaluation of emotions, and compared with faces with original facial or greenish color, reddish angry faces are often judged as having higher emotion intensity. Although perceptual modulation by the relationship between anger and red has also been reported from the perspective of electroencephalography (EEG), how variations in perceived emotion intensity are reflected in brain activity remains unclear. This study investigated whether EEG activity associated with face and facial expression processing is modulated as a function of the interaction between facial color and perceived emotion intensity. In the experiment, we recorded EEGs while participants evaluated emotion intensity using facial stimuli created by combining morph continua from neutral to angry expressions with three types of facial color conditions (original, red, and green). The results revealed that, in the red facial color condition, the early posterior negativity (EPN) amplitude significantly increased as a function of emotion intensity compared with those in the original and green facial color conditions. These findings suggest that the early, automatic affective processing of facial expressions, reflected in the EPN, is modulated by the combination of facial color and emotion intensity. Our findings provide new evidence that early, automatic affective processing of facial expressions, as indexed by the EPN, is modulated by the congruency between high anger intensity and a reddish facial color. HighlightO_LIReddish angry faces increase the ERP component associated with emotion evaluation. C_LIO_LIThe relationship between anger and red is evident in the left hemisphere. C_LIO_LIThe interaction between facial expression and color occurs at a later cognitive processing stage than facial expression or facial color processing alone. C_LI

neuroscience↗

bioRxiv2026

Exposure to Antibiotics Modifies the Immune Profiles of Bacterial Extracellular Vesicles from Common Vaginal Anaerobes

BackgroundThe female lower reproductive tract harbors a complex microbiome that plays a critical role in reproductive health. A vaginal microbiome dominated by Lactobacillus crispatus (LC; Community State Type (CST) I) supports vaginal health, whereas a microbiome enriched with anaerobic species, such as Gardnerella vaginalis (GV) and Mobiluncus mulieris (MM) (CST IV) is linked to bacterial vaginosis (BV) and adverse outcomes, including sexually transmitted infections, infertility, and preterm birth. Although antibiotics such as metronidazole and clindamycin are commonly prescribed to treat BV, recurrence rates remain high, and the impact of these treatments on bacterial extracellular vesicles (bEVs), critical mediators of host-microbe interactions, is poorly understood. ResultWe investigated how antibiotic treatment at a dose below minimum inhibitory concentration alters the production and immunomodulatory function of bEVs derived from GV, MM, and LC. Using nanoparticle tracking analysis, cytokine profiling, and TLR pathway analyses, we found that antibiotic treatment significantly enhanced the inflammatory properties of bEVs in a species- and antibiotic-specific manner. Notably, bEVs from antibiotic-exposed GV and MM cultures induced elevated cytokine responses in epithelial and immune cells, primarily through TLR2 activation for GV bEVs, and through both TLR2 and TLR5 activation for MM bEVs. While LC bEVs are typically non-inflammatory, exposure to metronidazole, even at a lower dose than what is used clinically, rendered them immunostimulatory, suggesting a potential unintended proinflammatory consequence of treatment on beneficial microbes. We also detected bEVs in human vaginal swabs, including vaginolysin-positive bEVs, even in CST I microbiomes, indicating that low-abundance microbes, including pathogens, remain transcriptionally active. ConclusionsThese findings suggest that antibiotics not only reduce microbial load but also reshape bacterial communication via bEVs, potentially contributing to inflammation, epithelial barrier disruption, persistent dysbiosis, and recurrent infections. This work underscores the need for precision antimicrobial strategies that eliminate pathogens while preserving beneficial bacteria and their functional bEVs. Future therapies may benefit from considering the ecosystem-wide effects of antibiotics on the vaginal microbiome and its bEV-mediated signaling network.

microbiology↗

bioRxiv2026

A genomic and proteomic characterization of mannan-degradable Bacillus sp. TTS1, isolated from Tomakomai Forest in Hokkaido

A challenge in using plant biomass is its highly recalcitrant nature, which makes it economically infeasible to utilize. In natural environments, various microbes, including bacteria and fungi, are reported to decompose plant cell wall materials such as cellulose and hemicellulose, and there may be undescribed microbes that contribute to the degradation of plant biomass. We focused on isolating novel plant biomass-degrading bacteria and screened more than 100 isolates from the Tomakomai experimental forest in Hokkaido, Japan. Among them, one novel Bacillus species was chosen for whole-genome sequencing. Comparative genomics and a carbon source utilization assay indicated that the isolate belongs to a subspecies of Bacillus subtilis, which we named B. sp. TTS1. Glucose, cellobiose, xylose, xylan, mannose, or mannan was used as the sole carbon source in the minimum medium, and the growth of this bacterium was determined. Furthermore, a proteomic analysis of B. sp. TTS1 was performed using culture supernatants from various polysaccharide-containing media. In the present study, several key enzymes involved in plant biomass degradation were identified, namely {beta}-1,4-mannanase and xylanase, and they were highly enriched in all tested polysaccharides.

microbiology↗

bioRxiv2026

Transcriptomic timeseries links hepatic gene expression to an early and self-limited systemic response to enteric infection

The liver receives microbe and host signals from the intestine via the portal vein, thereby connecting the gut to systemic physiology. Homeostatic control of the timing of systemic responses is critical to prevent the expansion and dissemination of gut microbes and to mitigate untoward effects from prolonged systemic inflammation, however these mechanisms remain enigmatic. Here, to determine the role of the liver in coordinating systemic immune responses to enteric infection, matched measurements of global gene expression profiles were collected from the murine liver and intestinal epithelium throughout the course of enteric infection and clearance of Citrobacter rodentium, a mouse model of infectious colitis. These data revealed metabolic suppression in the liver during the peak of infection and a long-lived immune signaling pattern in the colon associated with CD4 and CD8 T cell infiltration that persisted beyond the clearance of infection. Furthermore, an early inflammatory signal was detected in the liver that resolved before the peak of disease and pathogen colonization. This self-limited, early signal depended on the pathogens virulence program and correlated with the timing of a corresponding systemic response, including circulating TNF- and IL-6, key mediators of acute-phase proteins. These results uncover the temporal pattern of hepatic changes in response to the course of intestinal infection and provide correlative evidence that an early pulse of gene expression in the liver coordinates and limits the duration of the systemic acute-phase protein response. Author summaryLocalized infections can trigger systemic inflammatory responses that help limit infection. However, prolonged systemic inflammation risks tissue damage and disease. Thus, the timing of systemic immune reactions is critical to the balance between immunity and damage. Yet, knowledge of the pathways that link gut-localized infections to systemic immune tone is limited. Since the liver is anatomically central to the connection between the gut and circulatory systems, we hypothesized that monitoring the kinetics of liver gene expression throughout the natural course of an intestinal bacterial infection would provide a valuable resource and yield insight into the control of systemic immune tone. Critically, we identified a burst of liver cytokine signaling that occurred and resolved before peak pathogen burden and disease in the colon and predicted the circulating inflammatory response. We propose that this early and self-limited signal from the liver coordinates the timing of the systemic response, ensuring it occurs early enough to promote immunity and resolve before causing tissue damage.

immunology↗

bioRxiv2025

IGF2BP3 is essential for the growth heterogeneity of colorectal adenoma cells by regulating MYC

Adenoma is a major precancerous lesion in colorectal cancer (CRC), and the adenoma-carcinoma sequence is a well-known multistep progression to CRC caused by the accumulation of genetic mutations. On the other hand, the non-genetic mechanisms in the adenoma-carcinoma sequence remain largely unknown. In this study, organoids were established from 31 colorectal adenomas from 19 patients. Some adenomas showed heterogeneity in the proliferative potential of single cells, and this heterogeneity was regulated by non-genetic mechanisms. IGF2BP3 was identified as a differentially expressed gene between organoids with different growth patterns. IGF2BP3 positively regulated MYC expression at the transcriptional level and negatively regulated it at the translational level. This promoted high proliferative potential with high levels of oxidative phosphorylation, while allowing cells to avoid MYC-induced cell death. IGF2BP3 affected the tumorigenicity of mouse adenomas in vivo. Intra-tumor heterogeneity in growth potential is acquired at the precancerous stage in the adenoma-carcinoma sequence of colorectal carcinogenesis, and IGF2BP3 plays an important role in regulating MYC levels. These findings provide new insights into the non-genetic regulation of adenomas during CRC development.

cancer biology↗

bioRxiv2025

Positional identification of a candidate gene for MALE STERILITY 2 (MS2) by linkage mapping and transcriptomic data in Cryptomeria japonica D. Don

BackgroundJapanese cedar (Cryptomeria japonica D. Don) is a major plantation species in Japan, but its abundant pollen production is a primary cause of seasonal allergic rhinitis (pollinosis). To mitigate this public health issue, the use of male-sterile cultivars has been promoted. Five types of recessive male-sterile mutations (ms1-ms5) have been identified, and the causal genes and mutations for MS1 and MS4 have been elucidated. However, the gene responsible for MS2-type male sterility remains unknown. ResultsWe aimed to identify the candidate gene responsible for MS2-type male sterility using a map-based cloning strategy. High-resolution linkage mapping localized the MS2 locus to a 1.56 cM interval on linkage group 5, corresponding to an 8.64 Mb region of the reference genome. Ninety-one genes in this region were subjected to functional annotation, gene expression analysis, and mutation screening. Among these, a single gene, SUGI_0493010, encoding a GDSL-type esterase/lipase protein (GELP), fulfilled all three criteria: it showed homology to pollen development genes in Arabidopsis thaliana, was specifically expressed in male strobili, and carried a deleterious amino acid substitution (S40F) within the predicted catalytic domain in ms2 mutant. The same mutation was also detected in a heterozygous individual (Ms2/ms2) from a separate breeding population, whose genotype was confirmed through progeny testing. Structural annotation revealed that the affected serine residue lies within the conserved GDSL motif, suggesting a functional disruption of enzymatic activity. ConclusionsOur results strongly suggest that SUGI_0493010 (GELP) is the causal gene for MS2-type male sterility in C. japonica. This finding enhances our understanding of male sterility mechanisms in conifers and provides a valuable genetic resource for breeding pollen-free trees. The study also demonstrates the effectiveness of combining genetic mapping with transcriptomic and mutational data in forest tree genomics.

genomics↗

bioRxiv2025

Atlas of innate immune responses to experimental cholera and IL22 treatment demonstrates protection by mucus-secreting cells

The diarrheal disease cholera remains a global threat, but there is limited knowledge of the innate immune defenses in the small intestine that protect against the causative agent, Vibrio cholerae. Here, single-cell RNA-sequencing of epithelial and immune cells mapped gene expression patterns in the infant mouse small intestine and revealed changes in response to V. cholerae infection and prophylactic treatment with an IL22 Fc-fusion protein. Infection increased the abundance of an enterocyte subtype with high expression of defense-associated functions and stimulated production of IL22, a cytokine linked to epithelial integrity, from group 3 innate lymphoid cells. Administration of IL22Fc increased production of vibriocidal Reg3{beta} from enterocytes and the abundance of secretory lineage and Muc2-producing goblet cells, which secreted mucus into the intestinal crypts, impairing V. cholerae association with the epithelium. These IL22-mediated responses limited V. cholerae intestinal colonization and protected mice from diarrhea and death. Our findings suggest enterocyte specialization in mucosal defense. SummarySingle cell studies uncovered specialization of epithelial cells in intestinal defense. The epithelial cell-targeting cytokine IL22 protected mice from cholera by promoting the genesis of mucus secreting cells.

microbiology↗

bioRxiv2025

Foxp3 and BATF cooperatively direct cis-regulatory programs and gene expression for functional differentiation of Treg cells

Mechanisms by which diverse transcription factors (TFs) shape the heterogeneous transcriptional and epigenetic landscape of regulatory T (Treg) cells remain poorly understood. By investigating interactions between BATF and Foxp3 TFs, we discovered their cooperative roles in directing cis-regulatory programs and gene expression essential for differentiation of immunosuppressive effector Treg (eTreg) cells. Simultaneous single-cell chromatin accessibility and transcriptome profiling, combined with topic modeling, identified cis-regulatory elements and associated programs jointly regulated by these TFs in eTreg cells. Genome-wide mapping of Treg cell-specific BATF and eTreg cell-specific Foxp3 binding sites revealed their co binding at some of these cis-elements, synergistically enhancing accessibility and transcription. Furthermore, we provide evidence that Foxp3 interacts with specific TFs to orchestrate diverse cis-regulatory programs among Treg cell differentiation states. Thus, Foxp3 serves as a master, but context-dependent regulator, cooperating with other TFs, including BATF, to shape the heterogeneous cis regulatory and transcriptional landscape critical for functional Treg cell differentiation.

immunology↗

bioRxiv2025

Expanded gene targeting in RNA hacking with G-tract-supply Staple oligomer

RNA hacking (RNAh) is a gene regulation technology that employs a short oligonucleotide, termed a Staple oligomer, to induce the formation of RNA G-quadruplex structures on target mRNAs. While RNAh has the potential to target approximately 65% of human mRNAs, its applicability to the remaining genes is restricted by the sequence constraints. Herein, we present the G-tract-supply Staple oligomer (Gs-Staple oligomer), designed to expand the range of targetable mRNAs within the RNAh framework. Incorporating G-tracts into Staple oligomers alleviates the sequence constraints, enabling access to a broader range of mRNA targets. Gs-Staple oligomers effectively suppressed the translation of target proteins in mammalian cells and in vivo. Furthermore, the gene suppression could be precisely modulated by adjusting the linker length between the G-tracts. These findings have significantly expanded the versatility of RNAh, suggesting its potential for further development while highlighting its potential to be utilized as a nucleic acid-based tool for research and clinical medicine.

bioengineering↗

bioRxiv2025

Dynamic vs. Static Facial Color Changes: Evidence for Terminal Color Dominance in Expression Recognition

Facial color is closely linked to the perception of emotion, with reddish tones often associated with anger. While previous studies have shown that static reddish facial tones enhance this perception, it remains unclear whether dynamic changes in facial color further amplify this effect. This study investigated how variations in facial color influence the perception of expression using a judgment task that involved morphed facial stimuli (fearful to angry). The participants evaluated facial expressions under two conditions: faces with dynamic color changes and faces with static colors. Experiment 1 compared red (CIELAB a*+) faces to original-colored faces, and Experiment 2 compared green (a*-) faces to original-colored faces. Neither experiment revealed significant differences between dynamic and static facial colors. However, faces with a final reddish color (higher a* value) were more likely to be perceived as angry. These findings suggest that the final facial color influences the perception of anger independent of whether the color change is dynamic or static. Our findings support the idea that the recognition of anger is modulated by the relationship between an angry expression and the color red and provide a new perspective on facial color changes in the interaction between facial expression and facial color.

neuroscience↗

bioRxiv2024

Interaction between facial expression and color in modulating EPR P3

The relationships between facial expression and color affect human cognition functions such as perception and memory. However, whether these relationships influence attention remains unclear. Additionally, whether facial expressions affect selective attention is unknown; for example, reddish angry faces increase negative social evaluation or emotion intensity, but it is unclear whether selective attention is similarly enhanced. To investigate these questions, we examined whether event-related potentials for faces vary depending on facial expression and color by recording electroencephalography (EEG) data. We conducted an oddball task using stimuli that combined facial expressions (angry, neutral) and facial colors (original, red, green). The participants counted the number of times a rarely appearing target face stimulus appeared among the standard face stimuli. The results indicated that the difference in P3 amplitudes for the target and standard faces depended on the combinations of facial expressions and facial colors; the P3 amplitudes for red angry faces were greater than those for red neutral faces. Additionally, there was no significant main effect or interaction effect of facial expression or facial color on P1 amplitudes for the target, and there were significant main effects of facial expression only on the N170 amplitude. These findings suggest that the intensity of a humans selective attention to facial expressions varies according to the higher-order semantic processing of the relationship between emotion and color rather than simple facial expression or facial color effects individually. Our results support the idea that red color increases the human response to anger from an EEG perspective. Significance StatementIt remains unclear whether selective attention to faces is modulated by the relationships between facial expression and color. Using an oddball task and recording EEGs, we showed that the event-related potentials reflecting selective attention are modulated by the interaction between facial expression and facial color, although the interaction was not found at earlier ERP stages. These findings suggest that the intensity of selective attention to facial expressions is influenced more by the interaction between facial expression and facial color than by facial expression or facial color alone and that the interaction occurs as a higher-order processing step than facial expression or color recognition. Our results provide EEG evidence supporting the idea that red color increases the human response to anger.

neuroscience↗

bioRxiv2024

Developing simple DNA extraction and PCR-RFLP for MALE STERILITY 4 (MS4) gene in Cryptomeria japonica D. Don: Toward an environmentally friendly protocol

This study presents the development of a simple DNA extraction method and a novel PCR-RFLP protocol for genotyping the MALE STERILITY 4 (MS4) gene in Cryptomeria japonica as a proof of concept. Traditional CTAB-based DNA extraction methods, while effective, involve hazardous chemicals and require high-speed centrifugation, which are impractical in many field settings. Our approach utilizes a household dish detergent-based buffer, sodium chloride, and polyvinylpyrrolidone K-30 to extract DNA from C. japonica needle leaf tissues--without the need for liquid nitrogen. The simplicity of this method makes it more accessible and environmentally friendly. The extracted DNA was successfully used in PCR-RFLP analysis, targeting a single nucleotide polymorphism in the MS4 gene, demonstrating its efficacy for genotyping. The PCR-RFLP markers reliably discriminated between individual genotypes, confirming the practical application of our simple extraction method, even for conifers containing inhibitory substances. This technique is particularly advantageous for use in arboretums and field stations, where the use of hazardous chemicals, specialized equipment, and a draft chamber is limited. Our study contributes to genetic resource management by providing an easy, reliable, and safer method for DNA extraction and genetic analysis.

genetics↗

bioRxiv2024

Visual cues for moisture perception of facial skin: Enhancing high-frequency components of skin lightness increases perceived dryness

Facial skin texture provides crucial visual cues that reflect an individuals impressions and health conditions. In this study, we focused on the texture attribute of "moisture" and investigated which visual cues influenced skin moisture perception. The stimuli consisted of images from three facial areas (the whole face, cheek, and eyebrow areas) with and without makeup under two lighting directions. The participants rated the presented stimuli on the three texture attributes (moisture, glossiness, and attractiveness) using a five-point scale. The results from Experiment 1 revealed correlations between the ratings and histogram statistics of each channel in the CIELAB color space, with variations depending on the conditions and facial regions. A negative correlation was observed between the cheek moisture perception and the variance in the L* channel. We subsequently obtained similar ratings by enhancing the high-frequency components of skin lightness for artificially dried stimuli (Experiment 2) and for images depicting different skin conditions due to various types of makeup (Experiment 3). Both experiments confirmed a decrease in moisture and attractiveness and an increase in glossiness; these were correlated with the degree of artificial drying. These findings indicated that the high-frequency components of skin lightness could be visual cues for determining the perceived dryness.

neuroscience↗

bioRxiv2024

Evolution and diversification of the momilactone biosynthetic gene cluster in the genus Oryza

Plants are master chemists and collectively are able to produce hundreds of thousands of different organic compounds. The genes underlying the biosynthesis of many specialized metabolites are organized in biosynthetic gene clusters (BGCs), which is hypothesized to ensure their faithful co-inheritance and to facilitate their coordinated expression. In rice, momilactones are diterpenoids that act in plant defence and various organismic interactions. Many of the genes essential for momilactone biosynthesis are grouped in a BGC. Here, we apply comparative genomics of diploid and allotetraploid Oryza species to reconstruct the species-specific architecture, evolutionary trajectory, and sub-functionalisation of the momilactone biosynthetic gene cluster (MBGC) in the Oryza genus. Our data show that the evolution of the MBGC is marked by lineage-specific rearrangements and gene copy number variation, as well as by occasional cluster loss. We identified a distinct cluster architecture in O. coarctata, which represents the first instance of an alternative architecture of the MBGC in Oryza and strengthens the idea of a common origin of the cluster in Oryza and the distantly related genus Echinochloa. Our research illustrates the evolutionary and functional dynamics of a biosynthetic gene cluster within a plant genus.

plant biology↗

bioRxiv2023

Complex relationship among vessel diameter, shear stress and blood pressure controlling vessel pruning during angiogenesis

Blood vessel pruning during angiogenesis is the optimization process of the branching pattern to improve the transport properties of a vascular network. Recent studies show that part of endothelial cells (ECs) subjected to lower shear stress migrate toward vessels with higher shear stress in opposition to the blood flow for vessel regression. While dynamic changes of blood flow and local mechano-stress could coordinately modulate EC migration for vessel regression within the closed circulatory system, the effect of complexity of haemodynamic forces and vessel properties on vessel pruning remains elusive. Here, we reconstructed a 3-dimentsional (3D) vessel structure from 2D confocal images of the growing vessels in the mouse retina, and numerically obtained the local information of blood flow, shear stress and blood pressure in the vasculature. Moreover, we developed a predictive model for vessel pruning based on machine learning. We found that the combination of shear stress and blood pressure with vessel radius was tightly corelated to vessel pruning sites. Our results highlighted that orchestrated contribution of local haemodynamic parameters was important for the vessel pruning. Authors SummaryBlood vessel networks formed by angiogenic vessel growth subsequently undergo extensive vascular remodeling process by regression of selected vascular branches. Optimization of the branching pattern in the vasculature is critical to ensure sufficient blood supply throughout the entire tissue. Recent studies have highlighted a strong relationship between the vessel remodeling and the shear stress acting on the vessel wall. However, its detailed mechanisms remain elusive due to the difficulties of estimating local haemodynamic parameters and relating them to vessel remodeling. Here, we have numerically simulated local haemodynamic parameters within the vascular network of the postnatal day 6 (P6) mouse retinal vasculature. Then, the relationship among the local shear stress, blood pressure, and vessel radius with the vessel pruning was examined. Moreover, we developed a predictive model for the vessel pruning based on the local haemodynamic parameters by a machine learning technique. Importantly, our results indicate that the combination of shear stress and blood pressure with vessel radius is tightly correlated to vessel pruning sites. Given the ongoing clinical approach to suppress tumor growth via blood vessel normalization, our results provide important knowledge for developing future medicine such as nanomedicine based on drug delivery systems.

developmental biology↗

bioRxiv2023

Microglial cannabinoid receptor type1 mediates social memory deficits produced by adolescent THC exposure and 16p11.2 duplication

Adolescent cannabis use increases the risk for cognitive impairments and psychiatric disorders. Cannabinoid receptor type 1 (Cnr1) is expressed not only in neurons and astrocytes, but also in microglia, which shape synaptic connections during adolescence. Nonetheless, until now, the role of microglia in mediating the adverse cognitive effects of delta-9-tetrahydrocannabinol (THC), the principal psychoactive constituent of cannabis, has been unexplored. Here, we report that adolescent THC exposure produces microglial apoptosis in the medial prefrontal cortex (mPFC), which was exacerbated in the mouse model of 16p11.2 duplication, a representative copy number variation (CNV) risk factor for psychiatric disorders. These effects are mediated by microglial Cnr1, leading to reduction in the excitability of mPFC pyramidal-tract neurons and deficits in social memory in adulthood. Our findings highlight the importance of microglial Cnr1 to produce the adverse effect of cannabis exposure in genetically vulnerable individuals.

neuroscience↗

bioRxiv2023

Genetic and immune determinants of E. coli liver abscess formation

Systemic infections can yield distinct outcomes in different tissues. In mice, intravenous inoculation of E. coli leads to bacterial replication within liver abscesses while other organs such as the spleen largely clear the pathogen. Abscesses are macroscopic necrotic regions that comprise the vast majority of the bacterial burden in the animal, yet little is known about the processes underlying their formation. Here, we characterize E. coli liver abscesses and identify host determinants of abscess susceptibility. Spatial transcriptomics revealed that liver abscesses are associated with heterogenous immune cell clusters comprised of macrophages, neutrophils, dendritic cells, innate lymphoid cells, and T-cells that surround necrotic regions of the liver. Susceptibility to liver abscesses is heightened in the C57BL/6 lineage, particularly in C57BL/6N females. Backcross analyses demonstrated that abscess susceptibility is a polygenic trait inherited in a sex-dependent manner without direct linkage to sex chromosomes. As early as one day post infection, the magnitude of E. coli replication in the liver distinguishes abscess-susceptible and abscess-resistant strains of mice, suggesting that the immune pathways that regulate abscess formation are induced within hours. We characterized the early hepatic response with single-cell RNA sequencing and found that mice with reduced activation of early inflammatory responses, such as those lacking the LPS receptor TLR4, are resistant to abscess formation. Experiments with barcoded E. coli revealed that TLR4 mediates a tradeoff between abscess formation and bacterial clearance. Together, our findings define hallmarks of E. coli liver abscess formation and suggest that hyperactivation of the hepatic innate immune response drives liver abscess susceptibility. ImportanceAnimal models of disseminating bacterial infections are critical for developing therapeutic interventions. Following systemic dissemination in mice, E. coli undergo dramatic replication within abscesses in the liver but not in other organs. Although liver abscesses are the largest reservoir of bacteria within the animal, the processes that lead to abscess formation are not known. Here, we characterize E. coli liver abscess formation and identify several determinants of abscess susceptibility, including sex, mouse genotype, and innate immune factors. By combining spatial and single-cell transcriptomics with genetic and phenotypic analyses, we delineate critical host pathways that underlie abscess formation. Our findings define several avenues for future studies to unravel how abscess susceptibility determinants interact to modulate clearance of systemic infections and govern tissue-specific bacterial replication.

microbiology↗

bioRxiv2023

Inhibition of OCT4 Binding at the MYCN Locus Induces Neuroblastoma Cell Death Accompanied by Downregulation of Transcripts with High-Open Reading Frame Dominance

Amplification of MYCN is observed in high-risk neuroblastomas (NBs) and is associated with a poor prognosis. MYCN expression is directly regulated by multiple transcription factors, including OCT4, MYCN, CTCF, and p53 in NB. Our previous study showed that inhibition of p53 binding at the MYCN locus induces NB cell death. However, it remains unclear whether other transcription factors contribute to NB cell survival. In this study, we revealed that the inhibition of OCT4 binding at the MYCN locus, a critical site for the human-specific OCT4-MYCN positive feedback loop, induces caspase-2-mediated cell death in MYCN-amplified NB. We used the CRISPR/deactivated Cas9 (dCas9) technology to specifically inhibit transcription factors from binding to the MYCN locus in the MYCN-amplified NB cell lines CHP134 and IMR32. In both cell lines, the inhibition of OCT4 binding at the MYCN locus reduced MYCN activity. Differentially downregulated transcripts were associated with high-open reading frame (ORF) dominance score, which is associated with the translation efficiency of transcripts. These transcripts were enriched in splicing factors, including MYCN-target genes such as HNRNPA1 and PTBP1. Furthermore, transcripts with high-ORF dominance were significantly associated with genes whose high expression is associated with a poor prognosis of NB. In conclusion, the inhibition of OCT4 binding at the MYCN locus resulted in reduced MYCN activity, which in turn led to the downregulation of high-ORF dominance transcripts and subsequently induced caspase-2-mediated cell death in MYCN-amplified NB cells. Therefore, disruption of the human-specific OCT4-MYCN positive feedback loop may serve as an effective therapeutic strategy for MYCN-amplified NB. Contribution to the fieldNeuroblastoma (NB) is a childhood tumor. Amplification of MYCN is frequently observed in high-risk NBs and is linked to a poor prognosis. Multiple transcription factors, including OCT4, MYCN, CTCF, and p53, regulate MYCN expression by binding to the MYCN locus. This study investigated the contribution of these transcription factors in NB cell survival. We used CRISPR/deactivated Cas9 (dCas9) technology to specifically inhibit transcription factors from binding to the MYCN locus in MYCN-amplified NB cell lines. We found that the inhibition of OCT4 binding at the MYCN locus, a critical site for the human-specific OCT4-MYCN positive feedback loop, reduces MYCN activity and induces NB cell death. A detailed investigation of the molecular mechanisms of cell death revealed that the downregulated transcripts after suppressed MYCN activity were associated with high-open reading frame (ORF) dominance scores, which are associated with translation efficiency of transcripts. These transcripts were enriched in splicing factors, including MYCN-target genes such as HNRNPA1 and PTBP1. Reduced expression of these splicing factors altered the PKM mRNA splicing accompanied by the induction of p53-caspase-2-MDM2-mediated cell death. These findings suggest that disrupting the human-specific OCT4-MYCN positive feedback loop may serve as a promising therapeutic strategy for MYCN-amplified NB.

cancer biology↗