Biology subjects

Nakayama, H.

Publications and source records attributed to Nakayama, H..

17 recordsLinked to original sources

bioRxiv2026

Prohaptoglobin Promotes Pancreatic Cancer Progression by sustaining YAP Activity

Background & AimsProhaptoglobin (proHp), a precursor of haptoglobin (Hp), has recently emerged as a cancer-associated biomarker, but its functional role in pancreatic cancer remains unclear. We investigated whether proHp promotes malignant phenotypes of pancreatic cancer and explored signaling pathways involved. MethodsSerum proHp was examined in patients with pancreatic cancer and healthy controls. HP expression in pancreatic tumors and cell lines was analyzed using transcriptomic datasets. ProHp function was evaluated using PSN1 HP knockout (HPKO) cells, exogenous proHp supplementation, xenograft models, and RNA sequencing of PSN1 wild-type and HPKO cells. YAP activity was assessed by target gene expression, subcellular localization, YAP overexpression, and inhibition of YAP-TEAD interaction. ResultsSerum proHp was significantly elevated in patients with pancreatic cancer, and a subset of tumors and pancreatic cancer cell lines showed HP expression comparable to liver, indicating a tumor-derived source of proHp. In PSN1 cells, HPKO reduced motility, whereas exogenous proHp partially rescued this defect and enhanced motility in additional pancreatic cancer cell lines. Wild-type PSN1 cells continued to proliferate beyond confluence and formed rapidly growing xenograft tumors, which were abolished in HPKO cells. At high density, wild-type cells maintained YAP-related gene expression and nuclear YAP despite Hippo activation, whereas HPKO exhibited reduced nuclear YAP, indicating noncanonical YAP regulation by proHp. YAP restoration in HPKO cells rescued high-density proliferation and cell motility, while a YAP-TEAD inhibitor selectively reduced high-density proliferation of wild-type but not HPKO cells. ConclusionProHp promotes pancreatic cancer progression in a context-dependent manner by sustaining YAP activity and enabling cells to partially overcome contact-dependent growth inhibition. SynopsisProhaptoglobin, a precursor of haptoglobin, is elevated in pancreatic cancer and produced by tumor cells. It promotes cell motility, supports tumor growth under high-density conditions, and maintains YAP-dependent transcription that overrides contact-dependent growth inhibition. What You Need to Know BackgroundProhaptoglobin, a precursor of haptoglobin, is elevated in pancreatic cancer, but its tumor-derived origin and functional role are unknown. We examined whether prohaptoglobin drives progression by sustaining YAP signaling. ImpactWe show that tumor-derived prohaptoglobin sustains nuclear YAP activity, allowing pancreatic cancer cells to bypass contact inhibition and proliferate, revealing prohaptoglobin as a context-dependent driver rather than a passive biomarker. Future DirectionsDefining how prohaptoglobin engages upstream Hippo-YAP regulators and whether prohaptoglobin-YAP signaling is targetable in vivo may uncover new biomarkers and therapeutic vulnerabilities for pancreatic cancer.

cancer biology↗

bioRxiv2026

A live-imaging system for Arabidopsis leaf primordia at early stages

Live imaging is one of the most powerful methods to reveal the morphogenesis of plant organs. However, the highly three-dimensional structure of plant organs always poses technical challenges. For example, the basal region of leaf primordia is rarely observed because of the shape of leaf primordia and the sudden shift in geometry at the point where the leaf primordium connects to the hypocotyl. In this work, we developed a new live-imaging system that is suitable for observing the developmental process of the basal region of Arabidopsis leaf primordia at early stages. Using this system, we achieved continuous observation of the basal region of early Arabidopsis leaf primordia for more than 50 hours.

plant biology↗

bioRxiv2025

Order code in the olfactory system.

The ability to recognize odor identity across a wide range of concentrations is essential for natural olfactory behaviors. However, how odor identity is represented in the early olfactory system remains an open question. One theory proposes that glomeruli in the olfactory bulb, along with their associated odorant receptors (ORs), are activated by odorants in a temporal order that conveys information about odor identity. This order code is relatively robust to concentration changes, as the rank order of glomerular activation by a given odorant remains similar across concentrations. Alternatively, the primacy coding theory suggests that odor identity is defined by the most sensitive ORs, those that respond first, collectively referred to as the primacy set. To test these theories, we measured glomerular responses to a large set of odorants in the mouse olfactory bulb using calcium imaging. We found that receptor affinities can be embedded in a low-dimensional space (D = 10) with minimal loss of information. Within this space, we identified two clusters of glomeruli with distinct tuning properties that form independent odor representations. These clusters may correspond to the two phylogenetic classes of ORs, as revealed by both their functional characteristics and anatomical locations. In the OR affinity space, odorants evoke orderly activation waves whose directions can be used to define odor identities in the order coding model. Finally, we compared the order code and primacy model in predicting odor identity both across concentrations and across animals. Despite containing less information overall, the primacy model performed comparably to the order code. We confirmed the primacy models prediction that each receptor tends to contribute to the primacy set of at least one odorant. Analysis of binary odor mixtures revealed that mixture responses lie along geodesic lines connecting their component odors. Together, these findings suggest that odor information in the olfactory bulb may be represented through two complementary coding strategies: the primacy and order codes.

neuroscience↗

bioRxiv2025

Drought drives reversible disengagement of root-mycorrhizal symbiosis

The increasing frequency and severity of droughts pose a major threat to agriculture, food security and ecosystems. Plants respond to water deficit by adjusting growth and metabolism to enhance survival; these adjustments impact the soil microorganisms interacting with plant roots. Plants establish symbiotic relationships with arbuscular mycorrhizal fungi which supply soil nutrients in exchange for carbon metabolites via an intricate dual-species interface within roots. These fungi are dependent upon host-derived photosynthates and are thus potentially vulnerable to plant perturbations during drought. Here, we demonstrate that the plant-mycorrhizal relationship is dynamic when water becomes limiting. During water deficit, rice de-prioritizes nutrient acquisition gene regulatory networks, including its AM symbiotic program, in a strategy conserved with tomato. The fungal symbiont correspondingly represses its growth, undergoing metabolic quiescence, coupled with decommissioning of hyphae within the hosts root. Following re-watering, the host re-engages with its partner fungus, re-invigorating fungal growth and arbuscule establishment. This coordinate, reversible and enduring inter-organismal association may aid host survival under transient stress, but suggests that mutualisms in native and crop plants are potentially fragile in increasingly erratic climates.

plant biology↗

bioRxiv2025

Neuropilin 2 functions as a co-inhibitory receptor to regulate antigen-induced inflammation and allograft rejection

Co-inhibitory receptors function as central modulators of the immune response to resolve T effector activation and/or to sustain immune homeostasis. Here, using humanized SCID mice, we found that NRP2 is inducible on late effector and exhausted subsets of human CD4+ T cells and that it is co-expressed with established co-inhibitory molecules including PD-1, CTLA4, TIGIT, LAG3 and TIM3. In murine models, we also found that NRP2 is expressed on effector memory CD4+ T cells with an exhausted phenotype and that it functions as a key co-inhibitory molecule. Knockout of NRP2 resulted in hyperactive CD4+ T cell responses, and enhanced inflammation in delayed type hypersensitivity and transplantation models. Following cardiac transplantation, allograft rejection and graft failure was accelerated in global as well as CD4+ T cell-specific knockout recipients, and enhanced alloimmunity was dependent on NRP2 expression on CD4+ T effectors, and not on CD4+Foxp3+ T regulatory cells. Also, knockout T regulatory cells were found to be as efficient as wild type cells in the suppression of effector responses in vitro and in vivo. These collective findings identify NRP2 as a novel coinhibitory receptor and demonstrate that its expression on CD4+ T effector cells is of great functional importance in immunity.

immunology↗

bioRxiv2025

Simultaneous knockout of VITAMIN C DEFECTIVE 2 and 3 exacerbates ascorbate deficiency and light stress sensitivity

Light-dependent activation of ascorbate biosynthesis is essential for accumulating ascorbate to mitigate photooxidative stress. The VTC2 and VTC3 genes play key roles in this process: VTC2 encodes GDP-L-galactose phosphorylase (GGP), the rate-limiting enzyme in ascorbate biosynthesis, and VTC3 encodes a putative protein kinase/phosphatase with an unknown function. Here, we investigated their functional and genetic relationship. In vtc3 mutants, VTC2 transcription and GGP activity were slightly enhanced, suggesting that VTC3 is not required for VTC2 expression. Additionally, the vtc3 mutation had negligible effects on the transcriptome and the activity of enzymes involved in ascorbate redox cycle regulation, narrowing down the possible roles of VTC3 in ascorbate biosynthesis. Under low-light conditions, ascorbate levels were lower in vtc2 than in vtc3 mutants, but vtc2 retained the ability to increase ascorbate levels under high-light stress, unlike vtc3. The simultaneous knockout of VTC2 and VTC3 further reduced ascorbate levels compared to single mutants and severely impaired light stress-induced ascorbate accumulation, resulting in impaired non-photochemical quenching and enhanced photooxidative damage. These findings highlight the additive effects of VTC2 and VTC3 on ascorbate biosynthesis and stress tolerance. The vtc2 vtc3 double mutants provide a valuable model for further elucidating the physiological roles of ascorbate in plants.

plant biology↗

bioRxiv2025

Functional Impact of Glycosylation and Splicing Variants of LRIG1 on EGFR Proteostasis in Cancer

LRIG1, a membrane glycoprotein, has emerged as a significant stem cell marker and negative regulator of receptor tyrosine kinases (RTKs), including EGFR. Glycosylation is a major post-translational modification, which plays a crucial role in protein function and stability. In cancer biology, abnormal glycosylation can serve as a biomarker and contribute to pathogenesis. We aimed to investigate the effects of glycosylation on LRIG1 functions. Through database analysis and experimental approaches, we focused on evolutionarily conserved glycosylation sites of LRIG1, particularly N74 in humans. We found that a mutation of the N74 glycosylation site (N74Q) enhances LRIG1s binding to EGFR and promotes EGFR degradation. Furthermore, we identified a naturally occurring splice variant of LRIG1 lacking exon 2, which includes the N74 site, that shows similar enhanced EGFR binding and degradation. Analysis of TCGA data revealed that exon 2 skipping in LRIG1 occurs in various cancers, with higher levels correlating with poorer survival in breast and ovarian cancers. Our findings suggest that the absence of glycosylation at N74 enhances LRIG1-EGFR binding, providing an example of glycosylation negatively regulating protein-protein interaction. This mechanism, achieved through alternative splicing, provides insights into the importance of glycosylation deficiency in cancer biology.

biochemistry↗

bioRxiv2024

CD34-positive monocytes are highly susceptible to HIV-1

HIV-1 persists in cellular reservoirs despite effective combined antiretroviral therapy (cART). CD4+ T cells are a well-known reservoir, but there is evidence suggesting that myeloid cells, including circulating monocytes, are also a clinically relevant reservoir. However, it is not fully understood which subsets of monocytes are preferentially infected in vivo. Here, we show that a monocyte fraction expressing a stem cell marker CD34 is more susceptible to HIV-1 infection than the CD34-negative major subset. In cART-untreated viremic individuals, the CD34+ fraction increased in the percentage in total monocytes, and harbored higher copies of proviral DNA than the major subset. Consistent with this, the CD34+ fraction expressed HIV-1 receptors CD4 and CCR5 at higher levels and HIV-1 restriction factors MX2 and SAMHD1 at lower levels. Interestingly, proviral DNA was still detectable in the CD34+ fraction of cART-treated virologically suppressed individuals. CD34+ monocytes were also present in lymph nodes, and expressed CD4 and CCR5 at higher levels than the major subset, as observed in peripheral blood. Moreover, CD34+ monocytes present in peripheral blood and lymph nodes highly expressed CCR7 and sphingosine-1-phosphate receptor 1 (S1PR1), critical regulators of in vivo cellular trafficking. Collectively, our findings raise the new possibility that lymph node CD34+ monocytes, which originate from the circulation, are infected with HIV-1 owing to their high susceptibility to HIV-1, and return to circulation, which explains the detection of proviral DNA in peripheral CD34+ monocytes even after long-term cART.

immunology↗

bioRxiv2023

Ozone mediates tumor-selective cell death caused by air plasma-activated medium independently of NOx

Cold atmospheric plasma and plasma-treated liquids (PTLs) are emerging promising tools for tumor-targeted cancer treatment, as they preferentially injure tumor cells more than non-malignant cells. Oxidative stress is critical to the antitumor effect, but the oxidant mediating the effect is debatable. Previously, we reported that air plasma-activated medium (APAM) has tumor-selective cytotoxicity in vitro and in vivo. Moreover, an unusual mitochondrial positioning named monopolar perinuclear mitochondrial clustering (MPMC) and nuclear damage proceeds to cell death. We noticed that air plasma generation was accompanied by ozone (O3) formation, leading to suppose the possible role of O3 in the effect of APAM. In this study, we produced an O3-dissolved medium (ODM) and comparatively analyzed its biological effect with APAM. Both agents had comparable amounts of dissolved O3 (dO3), while APAM, but not ODM, contained nitrite and nitrate. Like APAM, ODM could induce apoptosis, nonapoptotic cell death, tubulin remodeling, MPMC, and nuclear shrinkage. Catalase mitigated all these events. The increases in various intracellular and mitochondrial reactive oxygen species (ROS) and lipid peroxides proceeded to cell death, and catalase also prevented them. Conversely, suppressing cellular H2O2 removal systems augmented mitochondrial ROS production and cell death. In contrast, like APAM, ODM minimally increased ROS production and MPMC in non-malignant cells. These results indicate that dO3 is a critical mediator of the actions of APAM, including tumor-selective induction of MPMC and cell death. Our findings suggest ODM could be a more chemically-defined alternative to PTLs in cancer treatment.

cancer biology↗

bioRxiv2023

Evolution of two gene networks underlying adaptation to drought stress in the wild tomato Solanum chilense

Drought stress is a key factor limiting plant growth and the colonization of arid habitats by plants. Here, we study the evolution of gene expression response to drought stress in a wild tomato, Solanum chilense naturally occurring around the Atacama Desert in South America. We conduct a transcriptome analysis of plants under standard and drought experimental conditions to understand the evolution of drought-response gene networks. We identify two main regulatory networks corresponding to two typical drought-responsive strategies: cell cycle and fundamental metabolic processes. We estimate the age of the genes in these networks and the age of the gene expression network, revealing that the metabolic network has a younger origin and more variable transcriptome than the cell-cycle network. Combining with analyses of population genetics, we found that a higher proportion of the metabolic network genes show signatures of recent positive selection underlying recent adaptation within S. chilense, while the cell-cycle network appears of ancient origin and is more conserved. For both networks, however, we find that genes showing older age of selective sweeps are the more connected in the network. Adaptation to southern arid habitats over the last 50,000 years occurred in S. chilense by adaptive changes core genes with substantial network rewiring and subsequently by smaller changes at peripheral genes.

evolutionary biology↗

bioRxiv2022

Chromosome-level genome assembly of Rorippa aquatica revealed its allotetraploid origin and mechanisms of heterophylly upon submergence

The ability to respond to environmental variability is essential for living systems, especially to sessile organisms such as plants. The amphibious plant Rorippa aquatica exhibits a drastic type of phenotypic plasticity known as heterophylly, a phenomenon where leaf form is altered in response to the surrounding environment. Although heterophylly has been studied in various plant species, its molecular mechanism has not been fully elucidated. To establish the genetic basis and analyze the evolutionary processes responsible for heterophylly, we assembled the chromosome-level genome of R. aquatica by combining data from Illumina short-read sequencing, PacBio long-read sequencing, and High-throughput Chromosome Conformation Capture (Hi-C) sequencing technologies. Fine-scale comparative chromosome painting and chromosomal genomics revealed that allopolyploidization and subsequent post-polyploid descending dysploidy occurred during R. aquatica speciation. The genomic information above was the basis for the transcriptome analyses to examine the mechanisms involved in heterophylly, especially in response to the submerged condition, which uncovered that the ethylene and blue light signaling pathways participate in regulating heterophylly under submerged conditions. The assembled R. aquatica reference genome provides novel insights into the molecular mechanisms and evolution of heterophylly.

plant biology↗

bioRxiv2021

Air plasma-activated medium exerts tumor-specific cytotoxicity via the oxidative stress-induced perinuclear mitochondrial clustering

Intractable cancers such as osteosarcoma (OS) and oral cancer (OC) are highly refractory, recurrent, and metastatic once developed, and their prognosis is still disappointing. Tumor-targeted therapy eliminating cancers effectively and safely is the current clinical choice. Since aggressive tumors have inherent or acquired resistance to multidisciplinary therapies targeting apoptosis, tumor-specific induction of another cell death modality is a promising avenue to meet the goal. Here, we report that a cold atmospheric air plasma-activated medium (APAM) can induce cell death in OS and OC via a unique mitochondrial clustering. This event was named monopolar perinuclear mitochondrial clustering (MPMC) because of the characteristic unipolar mitochondrial perinuclear aggregation. APAM had potent antitumor activity both in vitro and in vivo. APAM caused apoptosis, necrotic cell death, and autophagy. APAM contained hydrogen peroxide and increased mitochondrial ROS (mROS), while the antioxidant N-acetylcysteine (NAC) prevented cell death. MPMC occurred following mitochondrial fragmentation coinciding with nuclear damages. MPMC was accompanied by the tubulin network remodeling and mitochondrial lipid peroxide (mLPO) accumulation and prevented by NAC and the microtubule inhibitor, Nocodazole. Increased Cardiolipin (CL) oxidation was also seen, and NAC and the peroxy radical scavenger Ferrostatin-1 prevented it. In contrast, in fibroblasts, APAM induced minimal cell death, mROS generation, mLPO accumulation, CL oxidation, and MPMC. These results suggest that MPMC is a tumor-specific cause of cell death via mitochondrial oxidative stress and microtubule-driven mitochondrial motility. MPMC might serve as a promising target for exerting tumor-specific cytotoxicity. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=120 SRC="FIGDIR/small/466636v1_ufig1.gif" ALT="Figure 1"> View larger version (20K): org.highwire.dtl.DTLVardef@1118e2corg.highwire.dtl.DTLVardef@18cf99corg.highwire.dtl.DTLVardef@57a7edorg.highwire.dtl.DTLVardef@d1f447_HPS_FORMAT_FIGEXP M_FIG Graphical abstract C_FIG

cancer biology↗

bioRxiv2021

A behavioral paradigm for measuring perceptual distances in mice

Perceptual similarities between a specific stimulus and other stimuli of the same modality provide valuable information about the structure and geometry of sensory spaces. While typically a subject of behavioral experiments in humans, perceptual similarities, or distances, are rarely measured in other species. However, understanding the neural computations responsible for sensory representations requires the monitoring and sometime manipulating of neural activity, which is more readily achieved in other experimental models. Here we develop a behavioral paradigm that allows for the quantifying of perceptual similarity between sensory stimuli using mouse olfaction as a model system.

neuroscience↗

bioRxiv2021

Analysis of Classic Tomato Mutants Reveals Influence of Leaf Vein Density on Fruit BRIX

Tomato bipinnate (bip) is a classic leaf mutant, with highly increased leaf complexity resulting from the loss of function of a BEL-LIKE HOMEODAMAIN (BELL) gene. Here, we analyzed several bip mutants and their isogenic wildtype backgrounds for a suite of leaf morphology traits, ranging from leaf complexity, leaflet shape and size, to leaf vascular density to investigate how changes in leaf morphology influence fruit traits. Our analyses showed an unexpected relationship between leaf vein density and fruit sugar levels, where leaf vein density was negatively correlated with fruit BRIX. RNA-Seq analysis suggested variation in Glucose-6-phosphate translocator2 (GPT2) gene expression caused correlated changes in leaf vein density and BRIX when bip mutant and wildtype were compared, suggesting that the correlation between leaf vein density and fruit sugar may result from the genes regulating leaf vein development that are also involved in regulating leaf sugar biosynthesis. Our results provide a resource for further exploration of the genetic basis for the complex relationship between fruit quality and leaf traits in natural populations.

plant biology↗

bioRxiv2020

Leaf form diversification in an heirloom tomato results from alterations in two different HOMEOBOX genes

Domesticated plants and animals display tremendous diversity in various phenotypic traits and often this diversity is seen within the same species. Tomato (Solanum lycopersicum; Solanaceae) cultivars show wide variation in leaf morphology, but the influence of breeding efforts in sculpting this diversity is not known. Here, we demonstrate that a single nucleotide deletion in the homeobox motif of BIPINNATA, which is a BEL-LIKE HOMEODOMAIN gene, led to a highly complex leaf phenotype in an heirloom tomato, Silvery Fir Tree (SiFT). Additionally, a comparative gene network analysis revealed that reduced expression of the ortholog of WUSCHEL RELATED HOMEOBOX 1 is also important for the narrow leaflet phenotype seen in SiFT. Phylogenetic and comparative genome analysis using whole-genome sequencing data suggests that the bip mutation in SiFT is likely a de novo mutation, instead of standing genetic variation. These results provide new insights into natural variation in phenotypic traits introduced into crops during improvement processes after domestication.

plant biology↗

bioRxiv2019

Lignin-based resistance to Cuscuta campestris in tomato

Cuscuta species (dodders) are agriculturally destructive parasitic angiosperms. These parasitic plants use haustoria as physiological bridges to extract nutrients and water from hosts. Cuscuta campestris has a broad host range and wide geographical distribution. While some wild tomato relatives are resistant, cultivated tomatoes are generally susceptible to C. campestris infestations. However, some specific Heinz tomato hybrid cultivars exhibit resistance to dodders in the field, but their defense mechanism was unknown. Here, we discovered that the stem cortex in these resistant lines responds with local lignification upon C. campestris attachment, preventing parasite entry into the host. LIF1 (Lignin Induction Factor 1, an AP2-like transcription factor), SlMYB55, and CuRLR1 (Cuscuta R-gene for Lignin-based Resistance 1, a CC-NBS-LRR) are identified as crucial factors conferring host resistance by regulating lignification. SlWRKY16 is upregulated upon C. campestris infestation and acts as a negative regulator of LIF1 function. Intriguingly, CuRLR1 may play a role in signaling or function as a receptor for receiving Cuscuta signals or effectors to regulate lignification-based resistance. In summary, these four regulators control the lignin-based resistance response, preventing C. campestris from parasitizing these resistant tomatoes. This discovery provides a foundation for investigating multilayer resistance against Cuscuta species and has potential for application in other essential crops attacked by parasitic plants. One-sentence summaryFour key regulators confer lignin accumulation in the tomato stem cortex to block C. campestris host penetration upon infection.

plant biology↗

bioRxiv2019

Leaf shape is a predictor of fruit quality and cultivar performance in tomato

O_LICommercial tomato (Solanum lycopersicum) is one of the most widely grown vegetable crops worldwide. Heirloom tomatoes retain extensive genetic diversity and a considerable range of fruit quality and leaf morphological traits.\nC_LIO_LIHere the role of leaf morphology was investigated for its impact on fruit quality. Heirloom cultivars were grown in field conditions and BRIX by Yield (BY) and other traits measured over a fourteen-week period. The complex relationships among these morphological and physiological traits were evaluated using PLS-Path Modeling, and a consensus model developed.\nC_LIO_LIPhotosynthesis contributed strongly to vegetative biomass and sugar content of fruits but had a negative impact on yield. Conversely leaf shape, specifically rounder leaves, had a strong positive impact on both fruit sugar content and yield. Cultivars such as Stupice and Glacier, with very round leaves, had the highest performance in both fruit sugar and yield. Our model accurately predicted BY for two commercial cultivars using leaf shape data as input.\nC_LIO_LIThis study revealed the importance of leaf shape to fruit quality in tomato, with rounder leaves having significantly improved fruit quality. This correlation was maintained across a range of diverse genetic backgrounds and shows the importance of leaf morphology in tomato crop improvement.\nC_LI

plant biology↗