Biology subjects

Tanaka, E.

Publications and source records attributed to Tanaka, E..

17 recordsLinked to original sources

bioRxiv2026

Injury size regulates glucose allocation locally and systemically during vertebrate tissue regeneration

Tissue regeneration requires careful allocation of metabolic resources, yet how organisms adjust this allocation in response to varying amounts of tissue loss remains poorly understood. Here, we show that the regenerative metabolic response is not fixed: the size of an injury regulates how glucose is allocated at both local and organism-wide levels. We first demonstrate that tail regeneration requires glucose metabolism in the axolotl (Ambystoma mexicanum), a salamander capable of regenerating centimetre-scale tissues. We then mapped glucose uptake in axolotls regenerating from small or large tail injuries using positron emission tomography/magnetic resonance imaging (PET/MRI) and the radiolabelled glucose analogue [18F]FDG. Glucose uptake was elevated in regenerating tails compared to uninjured tails. During early regeneration, larger injuries induced higher glucose uptake than smaller injuries, correlating with faster regenerative outgrowth. Larger injuries also increased glucose uptake in distant organs, indicating a systemic metabolic response. Together, our findings suggest that metabolic responses tuned to injury size underlie faithful tissue regeneration and establish PET/MRI as a powerful approach for studying whole-body metabolic dynamics in large regenerating vertebrates.

developmental biology↗

bioRxiv2026

Senescence targeting re-enables injury-responsive repair in a human RPE aging model

Aging is associated with progressive tissue dysfunction and impaired repair after injury. In the retinal pigment epithelium (RPE), these changes contribute to age-related macular degeneration (AMD), yet the mechanisms limiting repair remain incompletely understood. Here, we establish a longitudinal human embryonic stem cell (hESC)-derived RPE aging model that recapitulates key features of aged human donor RPE and combine it with mosaic cell ablation to assess injury-responsive repair. Although aged RPE cells initiate DNA synthesis after injury, they exhibit impaired mitotic progression, uncoupling S-phase entry from epithelial repopulation. Transcriptomic profiling links this defect to a senescence-associated program marked by inflammatory signaling and suppressed mitotic networks. Pharmacologic reduction of senescent cells with Navitoclax shifts aged RPE toward a younger transcriptional profile but does not induce repopulation by itself. Instead, senolytic treatment primes aged RPE for repair, improving epithelial density and homeostatic function only in response to injury, a strategy we term "senolytic priming." These findings establish a human stem-cell-derived platform for investigating age-associated epithelial repair failure and show that aged human RPE retains latent repair capacity that can be re-enabled by targeting cellular senescence.

Cell Biology↗

bioRxiv2026

Field-based dissection of stomatal anatomy and conductance reveals stable QTL under drought and heat in wheat

Stomatal traits balance carbon gain with water loss, yet their breeding potential in wheat remains underexploited. This study investigated physiological and anatomical stomatal responses alongside yield across two years of large-scale field trials under water-limitation and delayed sowing-induced heat exposure. Across both seasons, stomatal conductance (gs) declined under stress, reflecting strong environmental constraint on gas-exchange (water-limitation:-26.9%; heat:-13.8%). Partitioning responses by leaf surface and genotype identified the adaxial surface as the dominant contributor to gs variation and the most stress responsive. Despite increases in theoretical anatomical gas-exchange capacity (gsmax), gs-efficiency declined, indicating partial decoupling between structural potential and realised conductance. Drought reduced stomatal size while increasing density whereas heat increased size, suggesting stress-specific anatomical plasticity. Moderate-to-high heritability was observed for anatomical traits (Water-limitation: 0.13-0.57; Heat: 0.42-0.71), contrasting with lower and less stable heritability for gs (water-limitation: 0.13-0.41; heat: 0.13-0.50). Genome-wide-association-mapping identified 169 putative QTLs, predominantly for anatomical traits, including stable and co-localised pleiotropic loci. Fourteen sets of closely positioned markers were detected across seasons or studies, with stable regions on chromosomes 2B, 3B and 7B emerging as key loci. Focusing on stable loci controlling adaxial stomatal anatomy offers a realistic strategy to enhance wheat photosynthetic efficiency and climate resilience. HighlightAdaxial stomatal traits dominate gas exchange responses to heat and drought in wheat, with stable anatomical QTL identified on chromosomes 2B, 3B and 7B. Their stability across environments supports their relevance for crop improvement in water-limited and high temperature systems.

physiology↗

bioRxiv2026

Versatile electroporation protocols enable reproducible CRISPR-RNP delivery across multiple primary mouse cells of the hematopoietic lineage

Genetic engineering of primary hematopoietic cells is essential for mechanistic immunology studies, however the development of cell-based therapies yet remains constrained by two major factors: the fragility of many primary lineages and challenges of viral delivery platforms that are costly, time-intensive, and biologically confounding. Here, we optimized scalable, non-viral CRISPR-Cas9 electroporation workflows using the ExPERT platform across three primary mouse hematopoietic cell types: OT-I CD8 T cells, bone marrow-derived macrophages (BMDMs), and hematopoietic stem cells (HSCs). In activated OT-I CD8 T cells, two electroporation programs supported high-efficiency mRNA and RNP delivery with minimal impact on cell viability or proliferative capacity, with subtle activation-state-dependent sensitivity at higher energy settings. Extending optimization to myeloid and stem cell lineages, we found that BMDMs maintained high viability following electroporation, and a high-performing electroporation program supported robust RNP delivery and efficient target gene knockout while preserving macrophage differentiation. In HSCs, the same program enabled consistent RNP delivery, sustained viability, and reproducible gene knockout. Together, these findings establish ExPERT electroporation as a robust, reproducible, and modular platform for non-viral genome editing across primary mouse hematopoietic lineages, lowering barriers to rapid genetic perturbation for both discovery and translational applications.

cell biology↗

bioRxiv2025

QTL for Heat-Induced Stomatal Anatomy Underpin Gas Exchange Variation in Field-Grown Wheat

Stomata are central to leaf gas exchange, governing carbon uptake, water loss, and ultimately, crop performance. However, the contribution of integrated stomatal anatomy and physiology to wheat heat tolerance remains poorly understood, particularly under realistic field conditions and across divers germplasm. This study explored the role of stomatal anatomical and physiological traits in shaping wheat responses to heat stress. Across two years of multi-environment field trials encompassing 200 genotypes in season 1 and 50 genotypes in season 2, we examined stomatal conductance (g), anatomical traits including stomatal size and density, and the stomatal conductance operating efficiency (gse) across leaf surfaces, along with grain yield. Timely and delayed sowing treatments were used to expose key developmental stages (anthesis) to contrasting temperature regimes. Early sowing supported higher gs and gse, while delayed sowing impaired stomatal function despite similar theoretical anatomical capacity (gsmax), revealing a decoupling of structural potential and physiological performance under stress. The adaxial surface consistently exhibited higher gs, stomatal density, and gsmax than the abaxial surface, highlighting its dominant role in leaf gas exchange. Later sowing induced plastic shifts in anatomy, including smaller, denser stomata, particularly on the adaxial surface, suggesting an adaptive response to thermal stress. Significant genotypic variation was observed for gs, gse, gsmax, and stomatal anatomical traits, with moderate heritability indicating genetic control. 125 putative QTL were identified for multiple stomatal traits across environments, including several stable loci on chromosomes 2B and 5B, and numerous closely clustered QTL for anatomical traits on chromosome 7B, highlighting key genomic regions underlying stomatal anatomy. In contrast, QTL for gs and gse were fewer and season-specific, highlighting the environmentally sensitive nature of physiological stomatal regulation. 42 of the QTL identified were consistent with previously reported QTL for stomatal traits in wheat. Together, these findings elevate the role of stomatal traits, supporting an integrated breeding strategy that combines selection for favourable stomatal anatomy with efficiency physiological regulation. Incorporating traits like gse into selection frameworks may enhance yield stability and resilience in heat-prone environments, advancing the development of climate-resilient wheat ideotypes. ScopeThis manuscript examines how stomatal anatomical and physiological traits integrate to shape wheat responses to heat stress under field conditions, addressing a central challenge in understanding the roles of stomata in a warming climate. Using multi-environment field trials across two growing seasons and encompassing 200 wheat genotypes, we quantify stomatal conductance (gs), anatomical traits, and stomatal operating efficiency (gse), across adaxial and abaxial leaf surfaces, and investigate whether these are under genetic control. The study provides mechanistic insight into the dynamic regulation of stomatal function by demonstrating a decoupling between anatomical capacity and physiological performance under heat stress, alongside plastic shifts in stomatal traits across sowing times. The identification of 125 candidate QTLs, including numerous stable and co-localised QTL across seasons, supports their incorporation into breeding programs aimed at enhancing resilience and yield stability. This work aligns with the Research Topic by elucidating mechanistic underpinnings of stomatal conductance regulation, bridging stomatal biology with applied crop improvement strategies. This work is critical to improving understanding of plant water relations and carbon uptake under future climate scenarios to ensure food security in a changing climate.

plant biology↗

bioRxiv2025

Functional rescue of critical-size bone defect using molecular network analysis of axolotl limb regeneration.

The salamander limb has served as a canonical model for successful regeneration that has yielded numerous molecular insights on its basic mechanism. Harnessing such information to induce regeneration in a non-regenerative setting has been a long-sought goal. The amputated salamander limb efficiently regenerates all of its missing bones, but paradoxically, a large bone gap without amputation - commonly called a Critical Size Defect (CSD) - is not regenerated, similarly to other vertebrates1. This non-regenerating injury provides a human-relevant setting to understand how to rescue lack-of-regeneration. Satoh and colleagues demonstrated in axolotl that transplantation of blastema cells from an amputated limb into a CSD yields cartilage bridging of the CSD2. This work provided a roadmap for rescuing the CSD. Here we asked, what are the crucial molecular differences in cells populating a regenerating blastema versus the CSD and can they be used to elicit CSD bridging? Previous genetic fate mapping and single cell transcriptomics showed that limb regeneration occurs via migration and dedifferentiation of fibroblastic, soft connective tissue (CT) cells that form a multipotent, skeletal stem cell 3, 4. Here using single cell transcriptomics and genetic fate mapping we found that the CSD is populated by CT cells that undergo a divergent molecular transition compared to the blastema. Using gene regulatory network (GRN) modeling, and lipid nanoparticle (LNP) delivery of mRNA we could express a single molecular factor, Wnt3a, to induce cartilage bridging of the CSD. Our results demonstrate the power of using molecular information from successful regeneration to rescue a non-regenerating injury.

cell biology↗

bioRxiv2025

Immunometabolic determinants of long-term response in leukemia patients receiving CD19 CAR T cell therapy

Although most patients with relapsed/refractory B-cell acute lymphoblastic leukemia (B-ALL) receiving CD19-targeted chimeric antigen receptor (CAR) T cell therapy achieve remission, loss of CAR T cell functionality and subsequent relapse remains an unmet therapeutic need. We applied an integrative approach to study the immunometabolism of pre- and post-infusion CD19-CAR T cells of patients with relapsed/refractory B-ALL. Pre-infusion CAR T cells of long-term responders (LTR) had increased oxidative phosphorylation, fatty acid oxidation, and pentose phosphate pathway activities, higher mitochondrial mass, tighter cristae, and lower mTOR expression compared to products of short-term responders. Post-infusion CAR T cells in bone marrow (BM) of LTR had high immunometabolic plasticity and mTOR-pS6 expression supported by the BM microenvironment. Transient inhibition of mTOR during manufacture induced metabolic reprogramming and enhanced anti-tumor activity of CAR T cells. Our findings provide insight into immunometabolic determinants of long-term response and suggest a therapeutic strategy to improve long-term remission.

immunology↗

bioRxiv2025

Innovations in spinal cord cell type heterogeneity across vertebrate evolution

Vertebrates display remarkable diversity of sensorimotor behaviors, each adapted to distinct ecological and survival demands. This diversity raises fundamental questions about the evolutionary origin of motor control: do conserved spinal circuits underlie these behaviors, and how have they diverged across species. Recent studies detail spinal cell-type architecture in mammals but comparable, high-resolution atlases of the non-mammalian spinal cord are lacking. Here, we compare spinal cord cell types between fish, frogs, mice and humans, spanning [~]450 million years of evolution. Across species, we define highly conserved programs of cell type specification that segregate spinal neurons into nearly identical cardinal classes during development. This contrasts with adult stages, when spinal cell-type composition selectively diverges for excitatory neuron subpopulations. Using spatial transcriptomics, we localize this species divergence to the superficial, dorsal spinal cord, where variant neuropeptide expression defines mammalian-specific cell types. The most dorsal spinal cord thus emerges as a recently evolved hub for sensory integration in mammals, a neospinal cord analogous to the neocortex.

neuroscience↗

bioRxiv2025

Notch coordinates self-organization of germ layers and axial polarity in cnidarian gastruloids

Dissociation and reaggregation experiments in several animal systems have revealed the stunning capacity of self-organization. Reaggregated early gastrula cells (here called gastruloids) of the sea anemone Nematostella vectensis are able to regenerate with only little delay whole organisms that are virtually indistinguishable from normal developing polyps. However, the molecular control underlying the restoration of body axis and germ layers remains largely unknown. To address this, we established a standardized protocol, which reproducibly generates gastruloids developing into polys with a single body axis. Here, we show that committed mesodermal and endodermal cells are sorted out to the surface of the aggregate, where mesodermal cells form clusters of about 30 cells. At a critical time point, one mesodermal cluster immigrates, along with peripherally attached endodermal cells. Thereby, the inner germ layer and the oral-aboral axis is established in one and the same process. Functional studies demonstrated that this polarization of the endodermal cells requires a feedback loop of Notch and Wnt signaling. The dissociation of the early embryo disrupts Notch signaling in the endodermal cells, which leads to transient adoption of an endomesodermal profile, marked by the expression of the mesodermal cadherin1 until the boundaries between the germ layer identities are re-established. Our results highlight distinct morphogenetic behaviors of mesodermal and endodermal cells and the hitherto unknown role of Notch signaling in germ layer boundary formation in self-organizing gastruloids. Conservation of Notch-mediated boundary formation between endoderm and mesoderm mirrors bilaterian mechanisms, demonstrating how adoption of ancestral regulatory networks governing morphogenesis likely enabled the diversification of metazoan body plans.

developmental biology↗

bioRxiv2025

Biosynthetic plasticity enables CD8+ T cell functional resilience under nutrient stress

Summary / AbstractTo maintain lineage-specific functions, cells must acquire and allocate nutrients across diverse cellular processes, even in metabolically-dysregulated environments. The mechanisms allowing CD8+ T cells to maintain immune function in perturbed environments are poorly understood. We find that CD8+ T cells adapt to nutrient stresses over time, reconfiguring gene-regulatory and metabolic networks to license functional recovery. Under acute stress, T cells reorient translational programming, limiting nutrient demand while prioritizing stress-sensitive metabolic and transcriptional responses. Within these responses, the transcription factors ATF4 and CEBPG jointly establish an adaptive metabolic program, promoting amino acid synthesis and uptake while maintaining mitochondrial anaplerosis. Despite diminished energetic capacity under environmental stress, this program prevents failure of central carbon metabolism, mitigating stress amplification and cellular dysfunction to potentiate anti-tumor immunity. Altogether, we demonstrate that biosynthetic plasticity via translational and metabolic reprioritization confers functional resilience to immune cells in unfavorable environments, offering novel strategies to enhance immunotherapies.

immunology↗

bioRxiv2024

Biocontrol of bacterial wilt disease using plant-associated bacterial communities in tomato

Host-protective or disease-suppressive microorganisms are anticipated as sustainable controls for crop diseases, such as bacterial wilt. However, the efficacy of biocontrol strategies is often limited by a lack of resilience under varying environmental conditions and interactions with native microbial communities in the field. In this study, we assembled a bacterial wilt-suppressive synthetic community (SynCom) in tomato, consisting of bacterial isolates derived from co-cultured microbial complexes associated with the plant. This SynCom demonstrates significant disease-suppressive effects against Ralstonia solanacearum in tomato seedlings under both axenic and soil conditions. Additionally, our findings suggest the existence of an optimal level of SynCom colonization in plants, which is critical for effective disease control. Furthermore, the SynCom exhibits direct antibiotic activity and immunogenic properties that enhance the production of defense-related secondary metabolites, thereby influencing the plant-associated microbiome. Our results provide an effective approach to constructing SynComs that exert disease-suppressive effects within microbial community contexts.

plant biology↗

bioRxiv2023

Inducing an oxidized redox-balance improves anti-tumor CD8+ T cell function

Cancer immunotherapy using antigen-specific CD8+ T cells depends on long-lasting anti-tumor function of the in vitro expanded T cells. T cell function is intricately linked to the activity of many metabolic pathways directly impacting the ability of CD8+ T cells to kill tumor cells. Metabolic conditioning in vitro better prepares CD8+ T cells for in vivo survival, tumor infiltration and tumor clearance. The mechanism underlying in vitro metabolic conditioning-induced augmented in vivo T cell function remains poorly understood. Here we show that metabolic conditioning of CD8+ effector T cells induces an oxidized cellular redox balance at least in part mediated by increased mitochondrial reactive oxygen species (ROS). This redox shift contributes to enhanced in vivo persistence and tumor clearance. In human tumour-infiltrating T cells, altering the redox balance ex-vivo reinvigorated pro-inflammatory cytokine production. Therefore, we believe that redox alterations present a targetable pathway to increase T cell-based anti-tumor immunotherapy efficacy.

immunology↗

bioRxiv2022

Skeletal muscle lineage is dispensable for appendage regeneration in axolotl

Regeneration of a complex appendage structure such as limb requires hierarchical coordination of multiple types of tissues. Muscles, as one of the major cell masses in limbs, have been reported recently to be critical to guide other tissue regeneration in planaria, but its function and relationship to other cells in vertebrate complex regeneration have been unclear. Here, we use Pax7 mutant axolotls, in which the limb muscle is developmentally lost, to investigate limb regeneration in the absence of skeletal muscle. We find that the pattern of regenerated limbs is normal in Pax7 mutants compared to the controls. Lack of muscles do not affect the proliferation of fibroblasts, another major population in limbs. Furthermore, using single cell RNA-sequencing, we demonstrate that the cell type composition in completely regenerated limbs in Pax7 mutants is similar to that in the controls, except the lack of cell types in muscle lineage. Our study reveals skeletal muscle is not required for the guidance of complex tissue regeneration in axolotls, and provides new views of the tissue hierarchy in vertebrate appendage regeneration.

cell biology↗

bioRxiv2022

Developmental cell fate choice employs two distinct cis regulatory strategies

In many developing tissues the patterns of gene expression that assign cell fate are organised by secreted signals functioning in a graded manner over multiple cell diameters. Cis Regulatory Elements (CREs) interpret these graded inputs to control gene expression. How this is accomplished remains poorly understood. In the neural tube, a gradient of the morphogen Sonic hedgehog allocates neural progenitor identity. Here, we uncover two distinct ways in which CREs translate graded Shh signaling into differential gene expression. In the majority of ventral neural progenitors a common set of CREs are used to control gene activity. These CREs integrate cell type specific inputs to control gene expression. By contrast, the most ventral progenitors use a unique set of CREs. These are established by the pioneer factor FOXA2, paralleling the role of FOXA2 in endoderm. Moreover, FOXA2 binds a subset of the same sites in neural and endoderm cells. Together the data identify distinct cis regulatory strategies for the interpretation of morphogen signaling and raise the possibility of an evolutionarily conserved role for FOXA2-mediated regulatory strategy across tissues.

developmental biology↗

bioRxiv2021

Topological morphogenesis of neuroepithelial organoids

Animal organs exhibit complex topologies involving cavities and tubular networks, which underlie their form and function. However, how topology emerges during organ morphogenesis remains elusive. Here, we combine tissue reconstitution and quantitative microscopy to show that trans and cis epithelial fusion govern tissue topology and shape. These two modes of topological transitions can be regulated in neuroepithelial organoids, leading to divergent topologies. The morphological space can be captured by a single control parameter which is analogous to the reduced Gaussian rigidity of an epithelial surface. Finally, we identify a pharmacologically accessible pathway that regulates the frequency of trans and cis fusion, and demonstrate the control of organoid topology and shape. The physical principles uncovered here provide fundamental insights into the self-organization of complex tissues.

biophysics↗

bioRxiv2018

Protective effects of low-intensity pulsed ultrasound on mandibular condylar cartilage exposed to mechanical overloading

The aim of this study was to examine the role of low-intensity pulsed ultrasound (LIPUS) exposure in the onset and early progression of temporomandibular joint (TMJ) osteoarthritis (TMJ-OA) induced by mechanical overloading. Fifteen-week-old male Wistar rats were divided into two experimental groups and a control group (n = 5 each). In the experimental groups, both TMJs were subjected to mechanical overloading by forced mouth opening using a jaw-opening device for 3 h/day for 5 continuous days. After mechanical overloading, TMJs in one experimental group were exposed to LIPUS for 20 min/day. After the experiments, mandibles were resected from the rats, and the condyles were processed. The bones were analyzed using high-resolution microcomputed tomography (micro-CT). The resected TMJs were also subjected to histological analysis and immunohistochemical staining. Micro-CT images of the mandibular condyle showed severe subchondral trabecular bone loss in the experimental group with overloading. Treatment with LIPUS after overloading resulted in decreased subchondral trabecular bone resorption. In TMJ sections from the experimental group with overloading, cell-free regions and proteoglycan loss characterized the cartilage degradation; LIPUS exposure restricted these changes in the mandibular condyle. Furthermore, the number of tartrate-resistant acid phosphatase-positive osteoclasts in the mineralized layer of the condylar cartilage increased after mechanical overloading and decreased after LIPUS treatment. Our findings suggest that LIPUS exposure after mechanical TMJ overloading downregulates subchondral trabecular bone resorption and proteoglycan loss in the mandibular condylar cartilage. Thus, it may prove to be protective effects of LIPUS exposure on onset and early progression of TMJ-OA induced by mechanical overloading.

developmental biology↗

bioRxiv2017

Signaling-dependent control of apical membrane size and self-renewal in rosette-stage human neuroepithelial stem cells

In the early developing nervous system, self-renewing neural stem cells are polarized and maintain an apical domain facing a central lumen. The presence of apical membrane is thought to have a profound influence on maintaining the stem cell state. With the onset of neurogenesis cells lose their polarization and the concomitant loss of the apical domain coincides with a loss of the stem cell identity. Very little is known about the molecular signals controlling apical membrane size. Here we use two neuroepithelial cell systems, one derived from regenerating axolotl spinal cord and the other from human ESCs to identify a conserved molecular signalling pathway initiated by lysophosphatidic acid (LPA) that controls apical membrane size and consequently controls and maintains epithelial organization and lumen size in neuroepithelial rosettes. This apical domain size increase occurs independently of effects on proliferation and involves a SRF-dependent transcriptional induction of junctional and apical membrane components.

neuroscience↗