Biology subjects

Hara, Y.

Publications and source records attributed to Hara, Y..

At least 19 recordsLinked to original sources

bioRxiv2026

Identification of a transient receptor potential channel that is regulated by phospholipid asymmetry

AbstractPhospholipid asymmetry is a hallmark of mammalian cell membranes and reflects the selective distribution of distinct phospholipid species between the two leaflets of the lipid bilayer. Although this asymmetry is tightly maintained, the membrane proteins whose functions depend on it remain largely unknown. To perturb phospholipid asymmetry experimentally, we expressed a constitutively active phospholipid scramblase and thereby identified transient receptor potential melastatin 8 (TRPM8) as an ion channel regulated by this membrane property. Activation of TRPM8 by both l-menthol and innocuous cold was markedly suppressed following disruption of phospholipid asymmetry. Likewise, selective depletion of phosphatidylserine (PS), a phospholipid enriched in the cytoplasmic leaflet, using a cytosolically targeted PS decarboxylase attenuated TRPM8 activation, indicating that cytoplasmic PS is required for proper TRPM8 function. Mechanistically, our findings suggest that cytoplasmic PS supports efficient TRPM8 activation by maintaining the biochemical state of the channel. Together, these findings identify TRPM8 as a phospholipid asymmetry-dependent ion channel and establish an experimental strategy for systematically identifying membrane proteins regulated by phospholipid asymmetry. This work provides a foundation for future studies investigating the biological significance of this fundamental membrane property.

biochemistry↗

bioRxiv2026

Dual Developmental Origins and Activity-dependent Specification of Mammalian Subplate Neurons

Subplate neurons (SpNs) are among the earliest-generated cortical neurons and are essential for neocortical circuit assembly. Despite this central role, they have long been considered a mammalian innovation, yet their evolutionary origin remains unresolved. Here, using comparative single-cell and spatial transcriptomics across amniotes (mice, chicks, and turtles), we identify two distinct developmental and evolutionary origins of SpNs: atypical SpNs (aSpNs), an Nr4a2-negative population conserved across amniotes and originating from the medial pallium, and mammalian-type SpNs (mSpNs), an Nr4a2-positive population preferentially expanded in mammals and arising from early-born cortical neurons. Cross-species analyses show that early-born pallial neurons in non-mammalian amniotes differentiate into thalamic input neurons, whereas this ancestral program is repurposed in mammals, with early-born neurons transiently adopting a subplate identity. We further show that this fate switch is controlled by Zbtb18 repression linked to thalamic input. Collectively, these findings establish a dual-origin model for SpNs and provide a unifying framework for understanding neocortical evolution. One-Sentence SummaryDevelopmental rewiring of an ancestral input-neuron program gave rise to the mammalian subplate.

evolutionary biology↗

bioRxiv2026

Biomechanical regulation of Ca2+ dynamics during muscle stem cell activation

Muscle satellite cells (MuSCs) are muscle-resident stem cells that are responsible for myofiber regeneration. Although the importance of calcium ions (Ca2+) in muscle physiology has been well established, the mechanism by which Ca2+ mobilization governs MuSC function remains poorly understood. In this study, we aimed to systematically characterize Ca2+ dynamics in MuSCs and to define the mechanisms regulating these signals during muscle regeneration. By employing modified protocols for mouse MuSC isolation and Ca2+ measurement, we observed spontaneous Ca2+ fluctuations in MuSCs isolated from regenerating muscle after cardiotoxin-induced myofiber injury. Our detailed analysis using chemical Ca2+ indicators and a genetically encoded Ca2+ indicator revealed that the frequency and amplitude of Ca2+ fluctuations increased significantly during the activated and proliferative stages of MuSCs in muscle regeneration. This effect was more pronounced in MuSCs isolated from dystrophic and aged mice. Mechanistically, these Ca2+ fluctuations were at least partially mediated by mechanosensitive ion channels, including PIEZO1 and TRPM7, which promote MuSC migration. Collectively, our findings demonstrate that Ca2+ fluctuations through mechanosensitive ion channels act as a key regulator of MuSC activation during muscle regeneration and may provide new insights into the role of Ca2+ influx in muscle biology and the pathogenesis of muscle diseases.

cell biology↗

bioRxiv2026

Molecular Crowding-Driven Nucleosome Interactions Revealed Through Single-Molecule Optical Tweezers

Molecular crowding causes the compaction of chromatin fibers, contributing to the formation of the nuclear architecture. However, the molecular mechanism of compaction under crowded conditions is not yet fully understood. In this study, we employed the single-molecule optical tweezer method to investigate the effect of molecular crowding on chromatin structure. Force-extension experiments on a 12-mer polynucleosome in the presence of different sizes and concentrations of polyethylene glycol (PEG) as a crowding agent showed that at low concentrations of low-molecular-weight (MW) PEG, the compaction of the polynucleosome was not significant. In this respect, nucleosomes predominantly remained separated, while DNA-histone interactions within individual nucleosomes were slightly stabilized. In contrast, high concentrations of high-MW PEG significantly promote internucleosomal interactions, leading to highly compact polynucleosome conformations. Under these conditions, approximately 30 pN of force was required to disrupt the internucleosomal interactions and release DNA; this force was 36% higher than that required for DNA unwrapping in the absence of PEG. These findings suggest that molecular crowding impacts cellular processes by mechanically regulating chromatin accessibility for regulatory proteins and the passage of motor molecules such as RNA polymerase. Significance StatementChromatin condensation is closely related to biological processes such as transcription and replication. Molecular crowding has recently attracted attention as a factor regulating chromatin condensation. In this study, we used the optical tweezer method to analyze the molecular mechanisms underlying chromatin condensation. We found that high-molecular weight and high-concentration crowders (polyethylene glycol) induced significant compaction, which involved internucleosomal interactions that markedly reduced DNA accessibility. Our results suggest that molecular crowding not only alters the condensation state, but also mechanically regulates chromatin accessibility.

biophysics↗

bioRxiv2026

Expanding and Decoding the Chemistry of Phospholipid Headgroup in Eukaryotes

Cellular membranes have diverse phospholipids, chemical differences in whose headgroups impact many biological processes. Phosphatidylcholine is an essential phospholipid for human health, but not universally required for life. The evolutionary mechanisms underlying phospholipid preferences remain poorly understood, due to the difficulty of investigating metabolite structure-activity relationships in a cellular context. Here, we developed a generalizable metabolic-rewiring method to manipulate phospholipid headgroups together and their biological effects. This approach utilizes synthetic media to hijack evolutionarily conserved phosphatidylcholine biosynthesis, leveraging xenobiotics as principal precursors for scalable headgroup transformations. By identifying over 100 artificial headgroups, we expanded the chemical diversity of xenobiotic phospholipids. Unexpectedly, we discovered that subtle headgroup alterations produced distinct mammalian cellular activities. We demonstrated that chemical headgroup modifications differentially elicited structure-dependent effects on phospholipid-protein interactions, calcium dynamics, transcriptomic profiles, and stem cell differentiation. Notably, cross-species comparison revealed that human and yeast cells have different headgroup preferences critical for cell life and death. As proof-of-concept, interactome analysis identified headgroup-sensitive human microproteins vital for mitochondrial respiration, but non-conserved in yeast. These results exemplify the evolutionary diversity of key phospholipid-protein interactions, illustrating why humans depend on phosphatidylcholine. Overall, our findings establish a programmable platform for elucidating and engineering phospholipid-driven cellular functions.

cell biology↗

bioRxiv2025

Identification of a novel small molecule facilitating HIV elimination by the "Shock-and-Kill" approach

The development of antiretroviral therapy (ART) has significantly improved the prognosis of people living with HIV (PLWH). However, reservoirs of latent viruses represent a major barrier to achieving a complete cure of HIV infection. To overcome the burden of viral latency, the "Shock-and-Kill" strategy employs latency-reversing agents (LRAs) to reactivate the virus and thus render it susceptible to elimination. Existing LRAs are not optimal and there is an unmet need for improvement. By screening a small molecule library, we identified the novel LRA candidate 2-HSB (2-hydrido-2,2-spirobi(1,3,2-benzodioxaphosphole)) which not only reactivates latent HIV provirus but also induces specific cytopathic effects in both monocytic and T lymphocytic latent HIV reservoirs. Thus, this novel compound represents a dual "shock and kill" agent, unlike known LRAs which are limited to the "shock". The probable involvement of HIV-1 tat protein may account for its selectivity. Although both shock and kill effects seemed to be regulated by spleen tyrosine kinase, they were independent of each other, indicating that neither activation-induced cell death nor cell death-induced reactivation was occurring. Crucially, 2-HSB induced viral transcription in ART-suppressed PLWH samples in vitro. Our findings present 2-HSB as a promising dual-action compound for the "Shock and Kill" strategy, demonstrating efficacy in both transformed cell lines and clinically-relevant primary samples. These results raise the possibility of distinguishing the mode of action of the two effects, potentially leading to the development of a single agent causing both HIV-1 reactivation and elimination and contributing to the improvement of treatment.

microbiology↗

bioRxiv2025

Tetraploid Caenorhabditis elegans embryos exhibit enhanced tolerance to osmotic stress

Polyploidy is a widespread phenomenon in development and evolution and is often associated with altered cellular physiology and developmental robustness. However, the influence of genome doubling on embryonic robustness to environmental stress remains poorly understood. Here, we investigated developmental traits and osmotic responses in tetraploid Caenorhabditis elegans embryos. Tetraploid animals exhibited enlarged body and tissue sizes and produced embryos with approximately 1.6-fold greater volume than diploids, accompanied by moderately delayed development and partial embryonic arrest. When exposed to a range of osmotic environments, both diploid and tetraploid embryos swelled or shrank in response to external osmolarity. Strikingly, tetraploid embryos at the early stage maintained normal cell division across a broader range of osmotic conditions than diploids. Quantitative analyses further revealed that tetraploid embryos exhibit reduced cytoplasmic mass density, largely reflecting lower protein concentration, while lipid and RNA levels remain unaffected. These compositional differences likely buffer volume fluctuations and underlie the enhanced osmotic tolerance of tetraploid embryos. Our findings demonstrate that genome doubling reshapes embryonic cellular physiology in a non-proportional manner to ploidy, thereby enhancing robustness during early development.

developmental biology↗

bioRxiv2025

Baculovirus-mediated gene transfer enables functional expression of PIEZO1 ion channel in isolated muscle satellite cells

Primary tissue stem cells are useful not only for basic cell biological research but also for therapeutic applications: however, their broader utility is often limited by technical challenges, such as a low efficiency of exogenous gene expression. PIEZO1 is a large mechanosensitive ion channel that plays an important role in muscle-resident stem cells, known as muscle satellite cells (MuSCs), during muscle regeneration. In this study, we developed a method for the ectopic expression of PIEZO1 in isolated MuSCs. Using a baculovirus vector system, we expressed PIEZO1 in myoblast C2C12 cells. Following optimization of the infection condition, we achieved robust PIEZO1 expression in isolated MuSCs during activated and differentiated states, with appropriate subcellular localization and ion channel activity. Importantly, the baculovirus-mediated PIEZO1 expression restored the reduced proliferative capacity of Piezo1-deficient MuSCs to a level comparable to wild-type cells, indicating that the exogenously expressed PIEZO1 is functionally equivalent to the endogenous protein. Overall, we established an efficient method for the transfer of the Piezo1 gene into isolated MuSCs, which should provide a versatile platform to study other large proteins in MuSCs. Summary StatementA baculovirus-based method was developed, enabling robust and functional PIEZO1 expression in isolated muscle satellite cells and providing a platform to study large proteins in isolated stem cells.

cell biology↗

bioRxiv2025

Anti-amyloid beta therapy resolves stroke recovery impairment caused by Alzheimer's disease

Stroke and dementia are common comorbidities and a growing concern causing disability in aging societies worldwide. Although anti-amyloid beta (anti-A{beta}) antibodies have recently been anticipated to relieve preclinical Alzheimers disease pathology, we discovered that post-stroke administration of anti-A{beta} antibodies restored neural repair for stroke recovery impeded by cerebral A{beta} accumulation. Neuronal recovery-associated gene expression for stroke recovery was considerably impaired even by slight A{beta} accumulation in murine and human brain. Slight A{beta} accumulation had less impact on neurons without stroke but caused a unique myeloid immunity after an ischemic stroke that enhanced the inflammatory cascades impeding neural repair for stroke recovery. Aducanumab administration after ischemic stroke prevented formation of this malignant myeloid immunity, resolving the impairment of post-stroke neural repair caused by cerebral A{beta} accumulation. Thus, our study has revealed the ability of anti-A{beta} therapies to restore functional recovery after a stroke with cerebral A{beta} accumulation.

neuroscience↗

bioRxiv2025

Rapid pronucleus assembly using cytoplasmic RNAs in fertilized eggs of Xenopus laevis

The size of the nucleus, which serves as the site for essential cellular functions such as replication and transcription, is dynamically altered to support these functions in response to the surrounding environment. During the brief cleavage period in metazoan embryos, the small, hypercondensed sperm nucleus with silenced chromatin undergoes a dramatic transformation into a large, round pronucleus with relaxed chromatin, enabling the activation of chromatin functions necessary for subsequent development. However, it remains unclear whether the egg cytoplasm-specific molecular environment plays a role in pronucleus assembly. In this study, we evaluated the impact of abundant RNAs in eggs on pronucleus assembly by utilizing a cell-free reconstruction of interphase nuclei in Xenopus laevis egg extract. We found that when RNA levels deviated from the conventional concentration, the growth rate of the interphase nucleus decreased. Additionally, the addition of RNAs led to a more dispersed chromatin distribution and the dissociation of sperm-specific nuclear proteins from the chromatin. These chromatin remodeling properties, which were reproducible with the introduction of cationic compounds, facilitated the incorporation of somatic histones into the chromatin in reconstructed nuclei. Based on these findings, we propose that cytoplasmic RNAs promote the rapid decondensation of negatively charged chromatin from a hypercompacted state and the removal of positively charged protamines from sperm chromatin via electrical interactions. This remodeling accelerates pronucleus assembly during the brief cleavage period following fertilization and promotes the rapid growth in nucleus size.

developmental biology↗

bioRxiv2024

Detection of triglyceride metabolism in white blood cells using a novel fluorescently labeled long chain fatty acid analogue

123I-15-(p-iodophenyl)-(R,S)-methyl pentadecanoic acid (123I-BMIPP) is a long-chain fatty acid (LCFA) analog developed to examine myocardial LCFA metabolism and has been used as a tracer for nuclear cardiology. However, its use is limited because of the specialized features of cardiac scintigraphy. In this study, a novel BMIPP-based probe, in which iodine-123 was replaced with a fluorescent compound, was used to extend the application of 123I-BMIPP to ex vivo analysis of fatty acid metabolism. To confirm that fluorescently labeled BMIPP-based probe (fluorescent BMPP) is effective for the detection of LCFA metabolism ex vivo, we performed fluorescence-activated cell sorting (FACS) analysis for the incorporation of fluorescent BMPP using white blood cells from human peripheral blood. FACS analysis showed that the incorporation of fluorescent BMPP into white blood cells was dose-dependent. Fluorescence intensities of cells incorporating fluorescent BMPP were attenuated after incubation in non-fluorescent BMPP medium, suggesting that these cells could export the probe. Neutrophils from a patient with primary triglyceride deposit cardiomyovasculopathy, a rare type of triglyceride (TG) metabolism disorders, showed lower BMPP export and was ameliorated after treatment with tricaprin. These results suggest that fluorescent BMPP could be imported to and exported from cells through the same mechanism as 123I-BMIPP, reflecting the mechanism that occurs for LCFAs during TG metabolism. This study shows that fluorescent BMPP has the potential to be used as a probe for the diagnosis of TG metabolic diseases ex vivo.

cell biology↗

bioRxiv2024

Multi-timescale neural adaptation underlying long-term musculoskeletal reorganization.

The central nervous system (CNS) can effectively control body movements despite environmental changes. While much is known about adaptation to external environmental changes, less is known about responses to internal bodily changes. This study investigates how the CNS adapts to long-term alterations in the musculoskeletal system using a tendon transfer model in non-human primates. We surgically relocated finger flexor and extensor muscles to examine how the CNS adapts its strategy for finger movement control by measuring muscle activities during grasping tasks. Two months post-surgery, the monkeys demonstrated significant recovery of grasping function despite the initial disruption. Our findings suggest a two-phase CNS adaptation process: an initial phase enabling function with the transferred muscles, followed by a later phase abandoning this enabled function and restoring a control strategy that, while potentially less conflicted than the maladaptive state, resembled the original pattern, possibly representing a good enough solution. These results highlight a multi-phase CNS adaptation process with distinct time constants in response to sudden bodily changes, offering potential insights into understanding and treating movement disorders. SIGNIFICANCE STATEMENTAfter major changes to the bodys mechanics, the nervous system adapts using strategies on multiple timescales. Our primate tendon transfer study shows that core muscle synergy groupings remain stable, reflecting a default to modular control. However, the activation of these synergies changes dramatically; an initial, rapid swap of their timing proves to be maladaptive, impairing motor function. This conflict is only resolved through the gradual development of slower, compensatory strategies over several weeks. This process highlights the fundamental tension the CNS faces when its reliance on stable motor modules conflicts with the need for flexible control, offering insights into neural plasticity and staged rehabilitation.

neuroscience↗

bioRxiv2024

Conserved loop of a phase modifier endows protein condensates with fluidity

Dipeptide repeats (DPRs) that are gene products from abnormal hexanucleotide repeat expansion in C9orf72 trigger amyotrophic lateral sclerosis (ALS) through unknown mechanism. This study highlights, importin Karyopherin{beta}2 (Kap{beta}2), which is responsible for nuclear transport and phase modification of RNA-binding proteins (RBPs), as a major DPR target. We demonstrate DPR accumulation in the nucleus via Kap{beta}2-mediated transport, which results in dose-dependent toxicity observed in nematode and yeast models. In vitro interaction studies exploiting chemical probe arrays and biophysical measurements reveal multivalent DPR binding to Kap{beta}2, including at the conserved acidic loop. Refractive index and fluorescence imaging coupled with biochemical assays unveiled that binding of excess DPRs to the acidic loop turns a phase modifier Kap{beta}2 into phase disrupter, resulting more condensed and viscous RBP condensates. Our findings provides molecular insight into C9orf72-ALS related to age and repeat expansion.

biochemistry↗

bioRxiv2024

Sustaining microglial reparative function enhances stroke recovery

Neurological symptoms after brain injury can remain as lifelong detrimental sequelae since most spontaneous brain recovery disappears within a few months after brain injury. Microglia play an essential role in recovery processes after brain injury; however, cellular and molecular mechanisms that diminish spontaneous brain functional recovery remain unknown. We discovered by cellular fate analysis that reparative myeloid cells remained in the post-stroke brain even after losing their reparative function. ZFP384 was identified as a pivotal transcriptional regulator that diminished recovery phase-associated gene expression in reparative myeloid cells, turning them into ruined cells which lost reparative functions. ZFP384 diminished the YY1-mediated chromatin interaction necessary for expressing recovery phase-associated genes. Antisense oligonucleotide against Zfp384 sustained the broad range of neural repair effects of myeloid cells and enhanced stroke recovery, even in the chronic phase of ischemic stroke recovery. Thus, therapeutics preventing the myeloid reparative immunity from reaching a ruined state sustains brain functional recovery.

pathology↗

bioRxiv2023

Ether phospholipids modulate somatosensory responses by tuning multiple receptor functions in Drosophila

Transient receptor potential (TRP) and PIEZO channels are known receptors for physical stimuli, such as temperature and mechanical touch, respectively, in sensory nerves. As these receptors are localized in the plasma membrane, the modulation of sensory receptor activity by plasma membrane lipids has recently attracted attention. In this study, we focused on ether phospholipids (ePLs), which are abundant in neurons, and analyzed their role in somatosensation using Drosophila as a model. Reduced mechanosensory behavior was observed with ePL synthesizing gene knockout or knockdown in mechano-sensitive PIEZO-expressing neurons. The activation of PIEZO channels was significantly augmented in the presence of ePLs. Furthermore, we observed that ePLs modulate the thermosensory behavior and reduce thermal threshold of the thermosensitive TRPA1 channels. Finally, we revealed that ePLs affect membrane tension and lipid order of the plasma membrane in culture cells. Our study identified ePLs as a modulator of multiple somatosensation modalities in Drosophila, which underscore the significance of functional interaction between membrane lipid and sensory channel proteins.

molecular biology↗

bioRxiv2023

ULK1-regulated AMP sensing by AMPK and its application for the treatment of chronic kidney disease

AMP-activated protein kinase (AMPK) is a central kinase involved in energy homeostasis. Increased intracellular adenosine monophosphate (AMP) levels result in AMPK activation through the binding of AMP to the {gamma}-subunit of AMPK. Recently, we reported that AMP-induced AMPK activation is impaired in the kidneys in chronic kidney disease (CKD) despite an increase in the AMP/ATP ratio. However, the mechanisms by which AMP sensing is disrupted in CKD are unclear. In this study, we identified mechanisms of energy homeostasis in which Unc-51-like kinase 1 (ULK1)-dependent phosphorylation of AMPK{gamma}1 at Ser260/Thr262 promotes AMP sensitivity of AMPK. AMPK activation by AMP was impaired in Ulk1-/- mice despite an increased AMP/ATP ratio. We also demonstrated that MK8722, an allosteric AMPK activator, activates AMPK in the kidneys of a CKD mouse model via a pathway that is independent of AMP sensing. MK8722 treatment significantly attenuates the deterioration of renal function in CKD and is a potential therapeutic option in CKD therapeutics.

molecular biology↗

bioRxiv2023

Spatial transcriptome of developmental mouse brain reveals temporal dynamics of gene expressions and heterogeneity of the claustrum

During the development of the mammalian cerebral cortex, numerous neurons are arranged in a six-layer structure with an inside-out fashion to form the neocortex and wire neural circuits. This process includes cell proliferation, differentiation, migration, and maturation, supported by precise genetic regulation. To understand this sequence of processes at the cellular and molecular levels, it is necessary to characterize the fundamental anatomical structures by gene expression. However, markers established in the adult brain sometimes behave differently in the fetal brain, actively changing during development. Spatial transcriptomes yield genome-wide gene expression profiles from each spot patterned on tissue sections, capturing RNA molecules from fresh-frozen sections and enabling sequencing analysis while preserving spatial information. However, a deeper understanding of this data requires computational estimation, including integration with single-cell transcriptome data and aggregation of spots on the single-cell cluster level. The application of such analysis to biomarker discovery has only begun recently, and its application to the developing fetal brain is largely unexplored. In this study, we performed a spatial transcriptome analysis of the developing mouse brain to investigate the spatiotemporal regulation of gene expression during development. Using these data, we conducted an integrated study with publicly available mouse data sets, the adult brains spatial transcriptome, and the fetal brains single-cell transcriptome. Our data-driven analysis identified novel molecular markers of the choroid plexus, piriform cortex, thalamus, and claustrum. In addition, we revealed that the internal structure of the embryonic claustrum is composed of heterogeneous cell populations.

developmental biology↗

bioRxiv2022

A novel fluorescently-labeled long-chain fatty acid analog for the study of fatty acid metabolism in cultured cells

123I-15-(p-iodophenyl)-(R,S)-methyl pentadecanoic acid (BMIPP) is a long-chain fatty acid (LCFA) analog developed to examine myocardial LCFA metabolism and has been used as a tracer for nuclear cardiology. However, its use is limited because of the specialized features of cardiac scintigraphy. In this study, a novel BMIPP-based probe was utilized, in which iodine-123 was replaced with a fluorescent compound, to extend the use of 123I-BMIPP to a wider variety of cells ex vivo. To confirm that this fluorescent LCFA analog (fluorescent BMPP) was imported into cells, fluorescence-activated cell sorting (FACS) analysis and fluorescent cell imaging were performed using cultured cells. The analysis showed that the import of fluorescent BMPP into the cells occurred in a concentration-dependent manner. This import into cells was inhibited by Sulfosuccinimidyl Oleate in a dose-dependent manner, which is an inhibitor of CD36, a well-known LCFA transporter, suggesting that fluorescent BMPP could be imported into cells via the same pathway as LCFA. FACS and cell imaging intensities of the cells importing fluorescent BMPP were attenuated after incubation in the non-Alexa680-BMPP medium. These results suggest that fluorescent BMPP can be transported into and from cells, reflecting the metabolism of LCFA. Fluorescently-labeled BMPP has the potential to be used as a probe for studying LCFA metabolism in various cells.

cell biology↗