Biology subjects

Takeuchi, Y.

Publications and source records attributed to Takeuchi, Y..

At least 19 recordsLinked to original sources

bioRxiv2026

Highly plastic macrophage niches orchestrate acquired quiescence and reactivation in breast-cancer bone metastasis

Recurrence and metastasis remain major causes of cancer mortality, sustained by therapy-resistant micrometastatic cells. Bone is a frequent site of breast-cancer relapse, yet the cues that reawaken disseminated cells remain poorly defined. We identify a previously unrecognized, highly plastic CXCL16 macrophage population that integrates tumor-associated macrophage programs found in distant metastatic sites such as lung and brain with non-tumor disease-associated traits in bone marrow. These CXCL16 macrophages establish a transient niche that restrains disseminated cancer-cell proliferation. Single-cell transcriptomics delineate functional remodeling of myeloid niches within the bone metastatic microenvironment: a CXCL16 macrophage niche that transiently constrains metastatic growth, and G-CSF macrophage and neutrophil niches that reignite tumor outgrowth. In primary tumors, cancer-associated fibroblasts (CAFs) aberrantly secrete G-CSF in response to cancer-cell signals, expanding G-CSF-receptor-positive subset of cancer cells with high metastatic potential. In advanced human bone metastases, CXCL16 macrophages localize to CAF-rich stroma but are excluded from cancer-cell clusters, indicating immune evasion. Together, these findings uncover CAF-bone-marrow cross-talk as a therapeutic target linking stromal inflammation, immune remodeling, and metastatic progression.

cancer biology↗

bioRxiv2026

Mitochondrial one-carbon enzyme MTHFD1L sustains stemness and metastatic progression in breast cancer

One-carbon (1C) metabolism is frequently upregulated in cancer to support anabolic growth and nucleotide biosynthesis. However, the contribution of mitochondrial 1C metabolism to cancer stemness and metastatic progression remains incompletely understood. Here, we identify methylenetetrahydrofolate dehydrogenase 1-like (MTHFD1L), a mitochondrial 1C metabolic enzyme, as a critical regulator of breast cancer stemness, tumor initiation, and lung metastasis. Genetic depletion of MTHFD1L in triple-negative breast cancer (TNBC) cell lines and patient-derived breast cancer models markedly impaired proliferation, sphere formation, tumorigenicity, and lung colonization. Metabolomic profiling revealed extensive metabolic rewiring following MTHFD1L loss, characterized by accumulation of the purine biosynthetic intermediates SAICAR and AICAR together with perturbations in glycolytic and pentose phosphate pathways. Importantly, suppression of lung metastasis was accompanied by reduced expression of the stemness-associated transcription factor SOX2 and decreased proliferative activity in metastatic lesions. Collectively, our findings establish MTHFD1L as a key metabolic dependency linking mitochondrial 1C metabolism to stem-like properties and metastatic progression in breast cancer, and highlight MTHFD1L as a promising therapeutic target in metastatic TNBC.

Cancer Biology↗

bioRxiv2026

GIRAF 1.0: A unified global framework to anticipate plant pest invasions

Plant pests threaten 10-40% of global food production, resulting in $55-220 billion in annual economic losses. Despite these escalating risks, biosecurity remains largely reactive, lacking anticipatory frameworks that integrate pest-specific drivers governing transboundary spread. We present GIRAF 1.0 (Global Invasion Risk Assessment Framework), the first quantitative, data-driven system that unifies pest-specific multi-host landscapes, abiotic suitability, and global trade networks with international phytosanitary policies. We applied GIRAF to four globally devastating pests - ranging from viral to insect taxa - to reconstruct a century of transcontinental spread and generate the first multiscale atlases of future invasion potential. GIRAF reveals that 22-37% of Earths land surface can contain host communities that largely overlap with environmentally suitable hotspots. Over 115 countries are highly vulnerable to trade-mediated pest introductions despite adopted phytosanitary policies. GIRAF provides a foundation for proactive surveillance and pandemic preparedness, offering a scalable path for transnational biosecurity agencies and global food industries.

ecology↗

bioRxiv2026

Immune Checkpoint Therapy Drives Maturation of a Cellular Neighborhood Nucleated by T Cell-APC Triads Enabling Spatially Compartmentalized Tumor Immunity

Spatially organized immune hubs of T cells and antigen-presenting cells (APCs) have been linked to immune checkpoint therapy (ICT) efficacy, yet the mechanisms underlying their function remain unclear. Using CODEX multiplex imaging, we longitudinally characterized the dynamic evolution of intratumoral cellular neighborhoods (CN) defined by "triad" interactions of CD4 and CD8 T cells with two distinct myeloid APC populations: cDC1s and IFN{gamma}-activated macrophages. We termed this CN the immunity-promoting CN (IP-CN) and tracked its progressive development during tumor rejection induced by -CTLA-4/-PD-1 therapy. A coordinated IFN{gamma} and TNF signaling signature accompanied the IP-CN assembly. Over time, the IP-CN underwent functional maturation, forming specialized sub-neighborhoods that compartmentalized proliferating T cells at the tumor periphery versus cytotoxic T effector cells interacting with tumor cell targets. Our findings reveal a spatiotemporal mechanism by which the IP-CN sustains and amplifies cytotoxic T cell responses, demonstrating how T cell-APC neighborhoods orchestrate tumor immunity.

immunology↗

bioRxiv2025

FoxO transcription factors couple the urea cycle and gluconeogenesis by controlling Ass1

Amino acid catabolism during fasting requires coordinated nitrogen disposal and glucose production, but the transcriptional logic linking the urea cycle to gluconeogenesis remains unclear. Forkhead box O (FoxO) transcription factors are key regulators of fasting metabolism, yet their role in controlling urea cycle genes has not been fully defined. Here we identify FoxOs as direct regulators of hepatic argininosuccinate synthase 1 (Ass1). Because FoxOs often act through Kruppel-like factor 15 (Klf15) in amino acid metabolism, we tested whether Ass1 regulation requires Klf15. Acute hepatic FoxO1/3a knockdown in fasted mice selectively reduced Ass1 expression, lowered blood glucose, and shifted urea-cycle amino acids, with arginine decreased and ornithine increased, even in Klf15-deficient livers. Silencing Ass1 phenocopied these metabolic effects, indicating that Ass1 mediates a key FoxO-dependent branch of fasting adaptation. Mechanistically, we mapped a functional FoxO-binding element within an upstream Ass1 enhancer: FoxO1/3a activated the enhancer in reporter assays, EMSA confirmed binding, and in vivo luciferase imaging and liver ChIP demonstrated fasting-inducible enhancer activity and FoxO occupancy. Collectively, these findings establish a FoxO-Ass1 axis that couples ureagenesis to gluconeogenesis and supports metabolic flexibility during fasting. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=158 SRC="FIGDIR/small/695746v1_ufig1.gif" ALT="Figure 1"> View larger version (23K): org.highwire.dtl.DTLVardef@94ff36org.highwire.dtl.DTLVardef@1ff4f3forg.highwire.dtl.DTLVardef@abd0e5org.highwire.dtl.DTLVardef@1f8d9b_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2025

Closed-loop heart rate regulation based on medulla stimulation

Cardiovasular diseases are often accompanied with the dysfunctions of autonomic nervous system. Cardiac neuromodulation including vagus nerve stimulation have emerged as alternative therapies by restoring sympatho-vagal balance. In this work, a medulla stimulation strategy was developed to precisely regulate the heart rate. The stimulation parameters effecting on cardiac function were assessed in open-loop experiments. The cardiac effects of rostral and caudal medulla stimulation were enhanced with increased stimulus frequency. We further investigated whether medulla stimulation can temporarily regulate the heart rate at predetermined levels using on-off closed-loop control. Additionally, we tested the capacity of medullary stimulation to rebalance autonomic function under peripheral imbalance conditions caused by dobutamine and neostigmine administration. The performance of heart rate regulation was quantified by the control degree and root mean squared error. The results demonstrate the feasibility of medulla stimulation for regulating sympathetic activity, emphasizing its potential therapeutic use in cardiac disorders.

physiology↗

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

A lipid-driven, microbe-independent mechanism of acne via Lrig1+ follicular progenitor cells

Long-chain saturated fatty acids (lcSFAs) are abundant in the skin, but their pathogenic roles in acne remain unclear. In human sebum profiling, C16:0, the most abundant lcSFA, was the only fatty acid significantly elevated in acne and correlated with inflammatory comedone counts. We then established a mouse model that faithfully recapitulates human acne phenotypes, in which topical C16:0 penetrated the epidermis and induced sebocyte hyperplasia, comedogenesis, and follicular inflammation. Mechanistically, C16:0 activated keratinization and inflammatory pathways and drove sebocyte-lineage differentiation from Lrig1+progenitor cells, which function as cutaneous lipid sensors. These effects persisted in germ-free mice and were unaffected by fatty acid transporter modulation, while MyD88 signaling was partially required for inflammatory cell recruitment. Together, our findings identified C16:0 as a human acne-associated lipid that recapitulates disease hallmarks through a microbe-independent, lipid-driven pathway, highlighting Lrig1+cells as central hubs in remodeling of the pilosebaceous unit.

cell biology↗

bioRxiv2025

Chronic social defeat causes dysregulation of systemic glucose metabolism via the cerebellar fastigial nucleus

Chronic psychological stress leads to hyperglycemia through the endocrine and sympathetic nervous systems, which contributes to the development of type II diabetes mellitus (T2DM). Higher plasma corticosteroids after stress is one well-established driver of insulin resistance in peripheral tissues. However, previous studies have indicated that only a fraction of patients with depression and post-traumatic disorder (PTSD) who develop T2DM exhibit hypocortisolism, so corticosteroids do not fully explain psychological stress-induced T2DM. Here, we find that chronic social defeat stress (CSDS) in mice enhances gluconeogenesis, which is accompanied by a decrease in plasma insulin, an increase in plasma catecholamines, and a drop in plasma corticosterone levels. We further reveal that these metabolic and endocrinological changes are mediated by the activation of neurons projecting from the cerebellar fastigial nucleus (FN) to the medullary parasolitary nucleus (PSol). These neurons are crucial in shifting the bodys primary energy source from glucose to lipids. Additionally, data from patients with depression reveal correlations between the presence of cerebellar abnormalities and both worsening depressive symptoms and elevated HbA1c levels. These findings highlight a previously unappreciated role of the cerebellum in metabolic regulation and its importance as a potential therapeutic target in depression, PTSD, and similar psychological disorders.

neuroscience↗

bioRxiv2025

Modeling of hepatitis B virus infection spread in primary human hepatocytes

Chronic hepatitis B virus (HBV) infection poses a significant global health threat, causing severe liver diseases including cirrhosis and hepatocellular carcinoma. We characterized HBV DNA kinetics in primary human hepatocytes (PHH) over 32 days post-inoculation (pi) and used agent-based modeling (ABM) to gain insights into HBV lifecycle and spread. Parallel PHH cultures were mock-treated or HBV entry inhibitor Myr-preS1 (6.25 g/mL) was initiated 24h pi. In untreated PHH, 3 viral DNA kinetic patterns were identified: (1) an initial decline, followed by (2) rapid amplification, and (3) slower amplification/accumulation. In the presence of Myr-preS1, viral DNA and infected cell numbers in phase 3 were effectively blocked, with minimal to no increase. This suggests that phase 2 represents viral amplification in initially infected cells, while phase 3 corresponds to viral spread to naive cells. The ABM reproduced well the HBV kinetic patterns observed and predicted that the viral eclipse phase lasts between 18 and 38 hours. After the eclipse phase, the viral production rate increases over time, starting with a slow production cycle of 1 virion per day, which gradually accelerates to 1 virion per hour after 3 days. Approximately 4 days later, virion production reaches a steady state production rate of 4 virions/hour. The estimated median efficacy of Myr-preS1 in blocking HBV spread was 91% (range: 90-92%). The HBV kinetics and the predicted estimates of the HBV eclipse phase duration and HBV production cycles in PHH are similar of those predicted in uPA/SCID mice with human livers. ImportanceWhile primary human hepatocytes (PHH) are the most physiologically relevant culture system for studying HBV infection in vitro, comprehensive understanding of HBV infection kinetics and spread in PHH is lacking. In this study, we characterize HBV viral kinetics and employ agent-based modeling (ABM) to provide quantitative insights into the HBV production cycle and viral spread in PHH. The ABM provides an estimate of HBV eclipse phase duration, HBV production cycles and Myr-preS1 efficacy in blocking HBV spread in PHH. The results resemble those predicted in uPA/SCID mice with human livers, demonstrating that estimated HBV infection kinetic parameters in PHH in vitro mirrors that observed in in vivo HBV infection chimeric mouse model.

systems biology↗

bioRxiv2024

Ca2+-evoked sperm cessation determines embryo number in mammals.

In mammals, fertilization takes place followed by fetus development in the maternal body, so the number of fetuses that exceeds the mothers capacity increases the frequency of stunted growth and stillbirths, while an excessive number of pups increases postnatal stunting and maternal child-rearing stress, which is detrimental to offspring procreation and species maintenance. Therefore, various control mechanisms are thought to be at work to ensure that fertilization occurs in appropriate numbers. Sperm are not capable of fertilization immediately after they are produced in the testis, and must undergo a stepwise activation process including capacitation, hyper motility activation or acrosome reaction before they meet the egg in the oviduct, where fertilization takes place, contributing positively on fertilization, which in turn ensures the number of fetuses for the maintenance of species. In contrast, in this study, we found that a subpopulation of sperm is derived in a Ca2+-dependent manner during the process for sperm to acquire fertility, which may regulate the number of fetuses. When sperm were harvested from the epididymis of mice and activated in vitro, a subpopulation of sperm emerged from the sperm population in which Lypd4 was expressed on the sperm surface at a ratio up to 30%. The sperm in this subpopulation were rather small in size, more permeable to dyes, and had already ceased motility. We further characterized this sperm population by surface antigen screening using various monoclonal antibodies and found the expression of several proteins, such as CD55, ICOS or Ccr3, specific to this population. The emergence of this sperm population was induced at a concentration of about 4% of Ca2+ in body fluids and was independent of capacitation or acrosome reaction, and also apoptotic process. This subpopulation also appeared over time in sperm ejaculated into the female body, accounting for about 50% of the sperm that reached the oviduct in an hour. When this sperm subpopulation was then removed from the entire population using anti-Lypd4 antibody followed by in utero insemination, the fertilization rate of the oocytes collected from the oviducts doubled. Such a sperm subpopulation was also observed in macaque monkeys, and removal of this subpopulation increased the egg penetration rate of sperm, suggesting that this sperm subpopulation exists commonly in mammals and that the mothers acceptable fetal number is adjusted by systematically sterilizing a certain number of sperm.

developmental biology↗

bioRxiv2024

TRPC6 is a mechanosensitive channel essential for ultrasound neuromodulation in mammalian brain

Ultrasound neuromodulation has become an innovative technology that enables non-invasive intervention in mammalian brain circuits with high spatiotemporal precision. Despite the expanding utility of ultrasound neuromodulation in the neuroscience research field and clinical applications, the molecular and cellular mechanisms by which ultrasound impacts neural activity in the brain are still largely unknown. Here, we report that transient receptor potential canonical 6 (TRPC6), a mechanosensitive non-selective cation channel, is essential for ultrasound neuromodulation of mammalian neurons in vitro and in vivo. We first demonstrated that ultrasound irradiation elicited rapid and robust Ca2+ transients mediated via extracellular Ca2+ influx in cultured mouse cortical and hippocampal neurons. Ultrasound-induced neuronal responses were massively diminished by blocking either the generation of action potential or synaptic transmission. Importantly, both pharmacological inhibition and genetic deficiency of TRPC6 almost completely abolished neuronal responses to ultrasound. Furthermore, we found that intracerebroventricular administration of a TRPC6 blocker significantly attenuated the population of neuronal firings in the cerebral cortex evoked by transcranial ultrasound irradiation in mice. Our findings indicate that TRPC6 is an indispensable molecule of ultrasound neuromodulation in the intact mammalian brains, providing fundamental understanding of biophysical molecular mechanisms of ultrasound neuromodulation as well as insight into its future feasibility in neuroscience and translational researches in humans.

neuroscience↗

bioRxiv2024

Label-free imaging of cellular organization in living mammalian cells via external apodization phase-contrast microscopy

Developing techniques to visualize intracellular structures, which influence the spatiotemporal functionality of biomolecules, is essential for elucidating mechanisms governing cellular behavior. In this study, we demonstrate that label-free external apodization phase-contrast (ExAPC) microscopy serves as a valuable tool for the simultaneous observation of various intracellular structures with high spatiotemporal resolution, while successfully mitigating halo artifacts. Additionally, through quantitative analysis of images obtained by combining ExAPC microscopy with fluorescence microscopy, we identified distinct heterogeneities in biomolecular condensates, lipid droplets, and mitochondria. Our findings highlight the potential of ExAPC microscopy to provide detailed insights into alterations in intracellular structures associated with diverse cellular processes, corroborating the existing knowledge and potentially contributing to the discovery of novel cellular mechanisms.

cell biology↗

bioRxiv2023

Selective elimination of CD169+ macrophages in lymph nodes invaded by breast cancers

Breast cancer cells suppress the host immune system to efficiently invade the lymph nodes; however, the underlying mechanism remains incompletely understood. Here, we report that metastasized breast cancer cells selectively eliminate CD169+ lymph node sinus macrophages, an initiator of anti-cancer immunity, from the lymph nodes. The comparison between paired lymph nodes with and without metastasis from the same patients demonstrated that the number of CD169+ macrophages was reduced in metastatic lymph nodes, whereas the numbers of other major immune cell types were unaltered. We also detected the infiltration of CD169+ macrophages into metastasized cancer tissues depending on sections, suggesting that CD169+ macrophages were gradually eliminated after anti-cancer reactions. Furthermore, CD169+ macrophage elimination was prevalent in major breast cancer subtypes and correlated with breast cancer staging. Collectively, we propose that metastasized breast cancer cells dispel CD169+ macrophages from lymph nodes in a phased manner, disabling a critical step of anti-cancer immunity.

cancer biology↗

bioRxiv2023

Early acquisition of S-specific Tfh clonotypes after SARS-CoV-2 vaccination is associated with the longevity of anti-S antibodies

SARS-CoV-2 vaccines have been used worldwide to combat COVID-19 pandemic. To elucidate the factors that determine the longevity of spike (S)-specific antibodies, we traced the characteristics of S-specific T cell clonotypes together with their epitopes and anti-S antibody titers before and after BNT162b2 vaccination over time. T cell receptor (TCR) {beta} sequences and mRNA expression of the S-responded T cells were investigated using single-cell TCR- and RNA-sequencing. Highly expanded 199 TCR clonotypes upon stimulation with S peptide pools were reconstituted into a reporter T cell line for the determination of epitopes and restricting HLAs. Among them, we could determine 78 S epitopes, most of which were conserved in variants of concern (VOCs). After the 2nd vaccination, T cell clonotypes highly responsive to recall S stimulation were polarized to follicular helper T (Tfh)-like cells in donors exhibiting sustained anti-S antibody titers (designated as "sustainers"), but not in "decliners". Even before vaccination, S-reactive CD4+ T cell clonotypes did exist, most of which cross-reacted with environmental or symbiotic bacteria. However, these clonotypes contracted after vaccination. Conversely, S-reactive clonotypes dominated after vaccination were undetectable in pre-vaccinated T cell pool, suggesting that highly-responding S-reactive T cells were established by vaccination from rare clonotypes. These results suggest that de novo acquisition of memory Tfh-like cells upon vaccination may contribute to the longevity of anti-S antibody titers.

immunology↗

bioRxiv2022

Deletion or inhibition of PTPRO mitigates diet-induced hepatic steatosis and inflammation in obesity

Chronic inflammation plays crucial roles in obesity-induced metabolic diseases. We herein demonstrated that mice lacking the protein tyrosine phosphatase receptor type O (PTPRO) exhibited the hyper-obese phenotype when fed a high-fat/high-sucrose diet. However, Ptpro-KO mice with hyperobesity showed the markedly small accumulation of ectopic fat in the liver, improvements in lipid and glucose homeostasis, and low-grade systemic inflammation associated with low macrophage activation. Expression of protein tyrosine phosphatase 1b (Ptp1b), an enzyme which is known to be implicated in metabolic disorders, was also suppressed in Ptpro-KO mice. The administration of AKB9778, a specific inhibitor of PTPRO, to highly obese ob/ob mice reproduced the phenotypes of Ptpro-KO mice along with the amelioration of inflammation. We revealed that an increase in the phosphorylation of Tyr(117) in vimentin, a component of intermediate filaments, by the inhibition of PTPRO promoted the growth of lipid droplets in adipocytes. The improvement in metabolic conditions with the attenuation of inflammation in Ptpro-KO mice was explained by the low activation of NF{kappa}b, a key transcription factor for inflammatory response, in adipose tissue. This is the first study to show that PTPRO is a promising target to ameliorate hepatic steatosis and metabolic disorders.

immunology↗

bioRxiv2022

Distantly related hepaciviruses share common entry factor, Claudin-1

Due to increased and broadened screening efforts, the last decade has seen a rapid expansion in the number of viral species classified into the Hepacivirus genus. Conserved genetic features of hepaciviruses suggest they have undergone specific adaptation and evolved to hijack similar host proteins for efficient propagation in the liver. Here, we developed pseudotyped viruses to elucidate the entry factors of GB virus-B (GBV-B), the first hepacivirus described in an animal, closely related to hepatitis C virus (HCV). GBV-B pseudotyped viruses (GBVBpp) were shown to be uniquely sensitive to the serum of tamarins infected with GBV-B, validating their usefulness as a surrogate for GBV-B entry studies. We screened GBVBpp infection of hepatoma cell lines CRISPR/Cas9-engineered to ablate expression of individual HCV receptors/entry factors and found that claudin-1 is essential for GBV-B infection, indicating GBV-B and HCV share a common entry factor. Our data suggest that claudin-1 facilitates HCV and GBV-B entry through distinct mechanisms since the former requires the first extracellular loop and the latter is reliant on the second extracellular loop. The implication of this sharing of claudin-1 as an entry factor between these two hepaciviruses on their tissue tropism and evolutionary relationships will be discussed. ImportanceHepatitis C virus (HCV) is a major public health burden; approximately 58 million individuals have chronic HCV infection which could lead to cirrhosis and liver cancer. To achieve the World Health Organisation target of eliminating hepatitis by 2030, new therapeutics and vaccines are needed. Understanding how HCV enters the cells will inform the design of new vaccines and treatments, targeting the first stage of HCV infection. However, the entry mechanism is complex and sparsely described. Studying the entry of related hepaciviruses will increase the knowledge of the molecular mechanisms of the first stages of HCV infection, such as the membrane fusion, and inform structure-guided HCV vaccine design; in this work we have identified a protein, Claudin-1, which facilitates the entry of HCV-related hepacivirus, but with a mechanism not described for HCV. Similar work on other hepaciviruses may unveil commonality of entry factors and possibly new mechanisms.

microbiology↗

bioRxiv2022

Single-cell transcriptome analysis reveals heterogeneity and a dynamic regenerative response of quiescent radial glia in adult zebrafish brain

In zebrafish telencephalon, radial glial cells (RGs) show a remarkable ability to regenerate damaged neural tissue by re-initiating cell proliferation to produce neural precursors to rebuild the lost neural circuit. However, it is not fully understood how RGs respond to brain damage to initiate this regenerative response. Here we applied single-cell transcriptomics to RGs in adult zebrafish telencephalon and identified five RG subtypes, which are classified into four quiescent RGs (qRGs) and one proliferating RG (pRG). The four qRGs differentially express distinct subsets of qRG markers, suggesting heterogeneity of qRG in zebrafish adult brain. Interestingly, one qRG subtype shows high expression of ribosomal proteins, and its fraction increases in response to brain damage. Consistently, the mTOR pathway is activated in RGs near the injury site. It was reported that inflammatory responses of brain-resident immune cells, microglia, are required for inducing regenerative responses of RGs in zebrafish. Genetical elimination of microglia not only suppressed the damage-induced regenerative response of RGs, but also decreased the fraction of the ribosomal expression-enriched qRGs. Our pseudo-time analysis suggests that putative dormant RGs produce ribosomal expression-enriched qRGs through activation of ribosomal genesis, as well as suppression of cholesterol biogenesis, and pRGs through activation of the JAK/STAT pathway. Our findings reveal heterogeneity of qRGs in adult zebrafish brain and their dynamic regenerative response to brain damage.

neuroscience↗