Biology subjects

Sasaki, T.

Publications and source records attributed to Sasaki, T..

At least 37 records · Page 2Linked to original sources

bioRxiv2025

Increased Genetic Protection Against Alzheimer's Disease in Centenarians

We constructed a polygenic protective score specific to Alzheimers disease (AD PPS) based on the current literature among the participants enrolled in five studies of healthy aging and extreme longevity in the US, Europe, and Asia. This AD PPS did not include variants on Apolipoprotein E (APOE) gene. Comparisons of AD PPS in different data sets of healthy agers and centenarians showed that centenarians have stronger genetic protection against AD compared to individuals without familial longevity. The current study also shows evidence that this genetic protection increases with increasingly older ages in centenarians (centenarians who died before reaching age 105 years, semi-supercentenarians who reached age 105 to 109 years, and supercentenarians who reached age 110 years and older). However, the genetic protection was of modest size: the average increase in AD PPS was approximately one additional protective allele per 5 years of gained lifetime. Additionally, we show that the higher AD PPS was associated with better cognitive function and decreased mortality. Taken together, this analysis suggests that individuals who achieve the most extreme ages, on average, have the greatest protection against AD. This finding is robust to different genetic backgrounds with important implications for universal applicability of therapeutics that target this AD PPS.

genetics↗

bioRxiv2025

Microstructural architecture of the argonauts' shell-like eggcase reveals the formation logic of a convergent extended phenotype

Argonautid octopods of the genus Argonauta possess a shell-like biomineralized external structure called an eggcase. A classical behavioral observation suggested that this structure is produced by the first dorsal arms rather than by the mantle tissue as seen in typical molluscan shells. In this study, we performed detailed microstructural analyses using scanning electron microscopy to investigate the characteristics of normal, undamaged eggcases and regions that had undergone post-damage repair. Our analysis revealed that the eggcase comprises five layers: an outermost organic membrane, an outer spherulitic-fibrous prismatic layer, a middle organic layer, an inner spherulitic-fibrous prismatic layer, and an innermost organic membrane. Both prismatic layers exhibit bidirectional growth from the middle organic layer, a unique feature not observed in typical molluscan shells. We propose a four-stage formation sequence to explain the observed microstructural architecture: nucleation on the organic scaffold, bidirectional crystal growth from the organic mid-layer, perpendicular growth relative to the eggcase surface, and final encapsulation by an organic membrane. Interestingly, the growth pattern and crystal shapes in the prismatic layers resemble of the internalized shells of cuttlefish, the calcified skeleton of stony corals, and avian eggshells, suggesting functional convergence. We also identified two repair mechanisms: reattachment of broken fragments and regeneration via new secretions. These findings call into question the previous assumptions about the role of the first dorsal arms in calcification. The eggcase also exemplifies the formation of a functionally and structurally complex extended phenotype through convergence.

zoology↗

bioRxiv2025

Proteomic profiling of tissue extracellular vesicles (EVs) identifies tissue-specific EV markers and predicts the accessibility of tissue EVs to the circulation

Extracellular vesicles (EVs) mediate cell-to-cell communication in endocrine, paracrine, and autocrine fashions, but their roles and transport in the body remain incompletely understood. It is expected that EVs circulate in the body through the bloodstream, where EVs derived from various tissues are present. However, how much each tissue contributes to circulating EVs is largely unknown. Therefore, identifying tissue-specific EV markers is of importance for elucidating in vivo dynamics of tissue EVs. A key issue that hampers studying EVs in vivo is the lack of methodologies for collecting them from tissues. Here, we developed methods to isolate EVs from four different tissues, skeletal muscle, heart, liver, and adipose tissue, and performed proteomic analysis on their EVs. Unbiased and quantitative proteomic analysis revealed protein signatures of EVs from the four tissues and identified marker proteins specific to EVs of each tissue. Furthermore, through comprehensive comparisons of the proteome from tissue and plasma EVs, we predicted the accessibility of EVs from the four tissues to the circulation. Our data suggests that, among the four tissues, adipose tissue-derived EVs more readily enter the circulation, while skeletal muscle-derived EVs exhibit poor accessibility to the blood. Collectively, our tissue EV proteome identified tissue-specific EV markers and suggests that the accessibility of tissue EVs to circulation highly depends on the original tissues.

physiology↗

bioRxiv2025

Fibroblast growth factor 21 regulates neuromuscular junctioninnervation through HDAC4 in denervation-induced skeletal muscle atrophy

Skeletal muscles undergo atrophy in response to denervation and neuromuscular diseases. Understanding the mechanisms by which denervation drives muscle atrophy is crucial for developing therapies against neurogenic muscle atrophy. Here, we identify muscle-secreted fibroblast growth factor 21 (FGF21) as a key inducer of atrophy following muscle denervation. In denervated skeletal muscles, FGF21 is uniquely upregulated among the FGF family members and acts in an autocrine/paracrine manner to promote muscle atrophy. Silencing FGF21 in muscle prevents denervation-induced muscle wasting by preserving neuromuscular junction (NMJ) innervation. Conversely, forced expression of FGF21 in muscle reduces NMJ innervation, leading to muscle atrophy. Mechanistically, TGFB1 released by denervated fibro-adipogenic progenitors (FAPs) upregulates FGF21 through the JNK/c-Jun axis, which in turn reduces the cytoplasmic level of histone deacetylase 4 (HDAC4), culminating in muscle atrophy. HDAC4 knockdown abolishes the atrophy-resistant effects observed in FGF21-deficient denervated muscles, resulting in muscle atrophy. Our findings reveal a novel role and heretofore unrecognized mechanism of FGF21 in skeletal muscle atrophy, suggesting that inhibiting muscular FGF21 could be a promising strategy for mitigating skeletal muscle atrophy.

biochemistry↗

bioRxiv2025

Transcription can be sufficient, but is not necessary, to advance replication timing

DNA replication timing (RT) is correlated with transcription during cell fate changes but there are many exceptions and our understanding of this relationship suffers from a paucity of reductionist approaches. Here, we manipulated length and strength of transcription in hybrid-genome mouse embryonic stem cells (mESCs) at a single locus upstream of the silent, late replicating, Pleiotrophin (Ptn) gene, directly comparing RT to nascent transcription rates at engineered vs. wild-type alleles. First, we inserted four reporter genes that differ only in their promoter. Two promoters transcribed the reporter gene at high rates and advanced RT. The other two transcribed at lower rates and did not advance RT. Since these promoters may prove useful in applications where effects on RT are undesirable, we confirmed the inability of one of them to advance RT at numerous ectopic sites. We next juxtaposed these same four promoters upstream of the Ptn transcription start site where they all transcribed the 96kb Ptn gene and advanced RT to different extents correlated with transcription rates. Indeed, a doxycycline-responsive promoter, which could not advance RT when induced as a small reporter gene, elicited a rapid and reversible RT advance proportional to the rate of transcription, providing direct evidence that transcription itself can advance RT. However, deletion of the Ptn promoter and enhancer, followed by directed differentiation to neural precursors, eliminated induction of transcription throughout the entire Ptn replication domain, without preventing the switch to early replication. Our results provide a solid empirical base with which to re-evaluate many decades of literature, demonstrating that length and strength of transcription is sufficient but not necessary to advance RT. Our results also provide a robust system in which to rapidly effect an RT change, permitting mechanistic studies of the role of transcription in RT and the consequences of RT changes to epigenomic remodeling.

genomics↗

bioRxiv2025

A CD57+ cytotoxic CD8 T cell subset associated with fibrotic lung disease in systemic sclerosis

Interstitial lung disease (ILD) is a major cause of morbidity and mortality in systemic sclerosis (SSc); however, the immunopathologic mechanisms driving lung disease in SSc are unclear. T cells have been implicated as a likely driver of lung injury in SSc. Here, we have evaluated T cells in blood and lungs of patients with SSc-ILD and identified a specific population of cytotoxic CD8 T cells that is expanded in SSc-ILD patients. Cytotoxic effector memory CD8 T cells marked by CD57 expression are preferentially expanded in SSc-ILD patients compared to SSc patients without ILD and controls and show prominent clonal expansion. These CD57+ T effector memory (TEM) cells differ from T effector memory cells re-expressing CD45RA (TEMRA) transcriptomically and functionally, with cytotoxic function that is enhanced by CD155 engagement of the costimulatory receptor CD226. Analyses of cells from ILD lungs indicate endothelial cells as a likely source of CD155 to activate CD57+ cytotoxic T cells. Together, the results implicate a CD57+ cytotoxic CD8 T cell population as a potential mediator of lung injury in SSc-ILD.

immunology↗

bioRxiv2025

Clonal relationships between Tph and Tfh cells in patients with SLE and in murine lupus

Pathologic T cell-B cell interactions drive disease in systemic lupus erythematosus (SLE). The T cells that activate B cell responses include T peripheral helper (Tph) and T follicular helper (Tfh) cells, yet the developmental and clonal relationships between these B cell-helper T cell populations are unclear. Here we use T cell receptor (TCR) profiling to demonstrate substantial clonal overlap between Tph and Tfh cells in the circulation of patients with SLE. Expanded Tph and Tfh cell clones persist over the course of 1 year in patients with a new diagnosis of SLE, and clones are observed to shift both from Tfh to Tph cells and from Tph to Tfh cells over time. High resolution analysis of cells sorted as Tph cells (CXCR5- PD-1hi) from SLE patients revealed considerable heterogeneity among these cells and highlighted a subpopulation of cells with transcriptomic features of activated B cell-helper T cells. This cell population, marked by expression of TOX and CXCL13, was found in both sorted Tph and Tfh cells, and was clonally linked in these two populations. Analysis of B cell-helper T cells in murine pristane-induced lupus demonstrated similar populations of Tph and Tfh cells in both lung and spleen with strong clonal overlap. T cell-specific loss of Bcl6 prevented accumulation of Tfh cells and reduced accumulation of Tph cells in pristane-treated mice, indicating a role for Bcl6 in the survival and expansion of both populations. Together, these observations demonstrate a shared developmental path among pathologically expanded Tph and Tfh cells in SLE. The persistence of expanded Tph and Tfh cells clones over time may explain the lack of stable tolerance induction by immunosuppressive medications or by B cell depletion.

immunology↗

bioRxiv2024

Control of Golgi- V-ATPase through Sac1-dependent co-regulation of PI(4)P and cholesterol

Sac1 is a conserved phosphoinositide phosphatase, whose loss-of-function compromises cell and organism viability. Here, we employed acute auxin-inducible Sac1 degradation to identify its immediate downstream effectors in human cells. Most of Sac1 was degraded in [~]1 h, paralleled by increased PI(4)P and decreased cholesterol in the trans-Golgi network (TGN) during the following hour, and superseded by Golgi fragmentation, impaired glycosylation, and selective degradation of TGN proteins by [~]4 h. The TGN disintegration resulted from its acute deacidification caused by disassembly of the Golgi V-ATPase. Mechanistically, Sac1 mediated TGN membrane composition maintained an assembly promoting conformation of the V0a2 subunit. Key phenotypes of acute Sac1 degradation were recapitulated in human differentiated trophoblasts, causing processing defects of chorionic gonadotropin, in line with loss-of-function intolerance of the human SACML1 gene. Collectively, our findings reveal that the assembly of the Golgi V-ATPase is controlled by the TGN membrane via Sac1 fuelled lipid exchange.

cell biology↗

bioRxiv2024

An integrated view of the structure and function of the human 4D nucleome

The dynamic three-dimensional (3D) organization of the human genome (the "4D Nucleome") is closely linked to genome function. Here, we integrate a wide variety of genomic data generated by the 4D Nucleome Project to provide a detailed view of human 3D genome organization in widely used embryonic stem cells (H1-hESCs) and immortalized fibroblasts (HFFc6). We provide extensive benchmarking of 3D genome mapping assays and integrate these diverse datasets to annotate spatial genomic features across scales. The data reveal a rich complexity of chromatin domains and their sub-nuclear positions, and over one hundred thousand structural loops and promoter-enhancer interactions. We developed 3D models of population-based and individual cell-to-cell variation in genome structure, establishing connections between chromosome folding, nuclear organization, chromatin looping, gene transcription, and DNA replication. We demonstrate the use of computational methods to predict genome folding from DNA sequence, uncovering potential effects of genetic variants on genome structure and function. Together, this comprehensive analysis contributes insights into human genome organization and enhances our understanding of connections between the regulation of genome function and 3D genome organization in general.

genomics↗

bioRxiv2024

Centromeric transposable elements and epigenetic status drive karyotypic variation in the eastern hoolock gibbon

Great apes have maintained a stable karyotype with few large-scale rearrangements; in contrast, gibbons have undergone a high rate of chromosomal rearrangements coincident with rapid centromere turnover. Here we characterize assembled centromeres in the Eastern hoolock gibbon, Hoolock leuconedys (HLE), finding a diverse group of transposable elements (TEs) that differ from the canonical alpha satellites found across centromeres of other apes. We find that HLE centromeres contain a CpG methylation centromere dip region, providing evidence this epigenetic feature is conserved in the absence of satellite arrays; nevertheless, we report a variety of atypical centromeric features, including protein-coding genes and mismatched replication timing. Further, large structural variations define HLE centromeres and distinguish them from other gibbons. Combined with differentially methylated TEs, topologically associated domain boundaries, and segmental duplications at chromosomal breakpoints, we propose that a "perfect storm" of multiple genomic attributes with propensities for chromosome instability shaped gibbon centromere evolution.

genomics↗

bioRxiv2024

Association Between Relational Mobility and DNA Methylation in Oxytocin Receptor Gene: A Social Epigenetic Study

DNA methylation is a type of epigenetic modification known to exhibit fluctuations in response to environmental factors. The association of macrosocial factors, such as interpersonal mobility, on methylation has seldom been investigated. This study aimed to examine the association of relational mobility, defined as the extent to which individuals can form and replace social relationships, on the DNA methylation of oxytocin receptor genes. DNA was extracted from the buccal cells of 95 adult participants (50 men and 45 women) and subjected to microarray analysis of DNA methylation using Illumina EPIC v2.0. The findings indicate that the oxytocin receptor genes methylation level was higher in individuals residing in low relational mobility social environments. The CpG site associated with relational mobility is an enhancer region, indicating that social environments with low relational mobility exert a suppressive effect on the transcriptional efficiency of the oxytocin receptor gene. Significance StatementThe association between DNA methylation of the oxytocin receptor gene and relational mobility was examined in 95 adults in their 20s to 60s, and found that those living in social environments with lower levels of relationship mobility had higher rates of DNA methylation of the oxytocin receptor gene. This study is a novel approach to a problem discussed in the social sciences using new analytical techniques in epigenomics.

genetics↗

bioRxiv2024

PDPN/CLEC-2 axis modulates megakaryocyte subtypes in a hematopoietic stem cell-regulating megakaryocyte-dominant manner

IntroductionMegakaryocytes are classified into several subtypes including LSP1-positive immune-skewed, MYLK4-positive hematopoietic stem cell (HSC)-regulating, and BMAL1-positive platelet-producing megakaryocytes. Podoplanin (PDPN)-expressing stromal cells generate a microenvironment that promotes megakaryopoiesis in the bone marrow. In this context, PDPN interacts with C-type lectin-like receptor-2 (CLEC-2) on megakaryocyte progenitors, which induces megakaryocyte proliferation. However, the megakaryocyte subtypes developed by the regulation of the PDPN/CLEC-2 axis have not yet been elucidated. Materials and MethodsWe established an immortalized bone marrow PDPN-expressing stromal cell line and a PDPN-knockout line (PDPN WT and KO feeder cells, respectively). Bone marrow hematopoietic progenitors were committed to megakaryocytes in co-culture with PDPN WT or KO feeder cells. The number and ploidy of megakaryocytes, resultant platelets, and the polarization of megakaryocyte subtypes were investigated. ResultsThe number of megakaryocytes was significantly increased in the co-culture with PDPN WT feeder cells compared to that with PDPN KO feeder cells. The megakaryocytes on the PDPN WT and KO feeders showed their main ploidy at 16N[~]32N and 8N[~]16N, respectively. The number of platelets decreased in the co-culture with the PDPN WT feeder compared to those in the co-culture with the PDPN KO feeder. Megakaryocyte subtypes were immunocytochemically detected in in vitro differentiated CD41-positive megakaryocytes. For each megakaryocyte subtype, the percentage of MYLK4-positive megakaryocytes significantly increased and the percentage of BMAL1-positive megakaryocytes significantly decreased when co-cultured with the PDPN WT feeder. ConclusionThe PDPN/CLEC-2 axis modulates megakaryocyte subtype differentiation, with a predominance of HSC-regulating megakaryocytes.

cell biology↗

bioRxiv2024

Defining a Muscle Stem Cell matrisome signature: from transcriptome data to extracellular matrix niche topology.

Although intensively investigated, the regulation of skeletal muscle stem cells (MuSCs) by their niche remains an open question. The extracellular matrix (ECM) components of the niche represent a dynamic microenvironment that undoubtedly participates in MuSCs behavior. We used bioinformatics analysis of transcriptomic data to define the matrisome profile of skeletal muscle resident cells, comprising genes encoding ECM and ECM-associated proteins. We identified quiescent MuSCs as key ECM producers of the niche, notably through the expression of specific basement membrane genes as Col19a1 and Lama3 and regulators of ECM assembly, Thsd4 and Aebp1. Unexpectedly, quiescent MuSCs also expressed matrisome neurogenesis-related genes. Immunofluorescence staining of selected ECM components showed their organization in isolated murine myofiber bundles. Upon activation, MuSCs strikingly downregulated the niche-related ECM genes and instead expressed genes involved in basement membrane disruption and matrisome genes linked to cell motility. This study identified distinct matrisome signatures of quiescent and activated MuSCs that are consistent with their function in homeostasis and repair of damaged skeletal muscle.

cell biology↗

bioRxiv2024

Transcriptome Analysis Identified SPP1+ Monocytes as a Key in Extracellular Matrix Formation in Thrombi

Thrombi follow various natural courses. They are known to become harder over time and may persist long-term; some of them can also undergo early spontaneous dissolution and disappearance. Hindering thrombus stability may contribute to the treatment of thrombosis and the prevention of embolisms. However, the detailed mechanisms underlying thrombus maturation remain unknown. Using RNA sequencing, we revealed the transcriptional landscape of thrombi retrieved from the cerebral vessels and identified SPP1 as a hub gene related to extracellular matrix formation. Immunohistochemistry confirmed the expression of osteopontin in monocytes/macrophages in the thrombi, particularly in older thrombi. Single-cell RNA sequencing of thrombi from the pulmonary artery revealed increased communication between SPP1-high monocytes/macrophages and fibroblasts. These data suggest that SPP1-high monocytes/macrophages play a crucial role in extracellular matrix formation in thrombi and provide a basis for new antithrombotic therapies targeting thrombus maturation. TeaserSPP1+ monocytes play a key role in thrombus maturation, which can be a potential target for novel antithrombotic therapies.

molecular biology↗

bioRxiv2024

Heart rate changes related to risky selections and outcomes in a rat gambling task

Risk-taking behavior is crucial for animals to increase their potential outcomes and is considered to alter arousal states in the brain and body represented by heart rates. In this study, we monitored changes in heart rate as rats performed a gambling task in which they selected either a certain outcome with 100% probability (sure option) or a probabilistic double outcome with 50% probability (risky option). We found that when rats selected risky options, they exhibited significantly greater decreases in their instantaneous heart rates immediately before selection than when they selected certain options. In addition, we observed significantly larger increases in instantaneous heart rates when the rats were informed of the larger number of outcomes after selecting the risky options than after selecting the sure options. These results demonstrate that animals can dynamically alter their instantaneous heart rates in response to risky selection and outcomes.

animal behavior and cognition↗

bioRxiv2024

Cell-based assays and comparative genomics revealed the conserved and hidden effects of Wolbachia on insect sex determination

It is advantageous for maternally transmitted endosymbionts to skew the sex ratio of their hosts toward females. Some endosymbiotic bacteria such as Wolbachia cause their insect hosts to exclusively produce female offspring through male killing or feminization. In some lepidopteran insects, male killing is achieved by affecting the sex-determining process in males, and a unique mechanism of male killing and its functional link with feminization have been implicated. However, comparative analysis of these phenotypes is often difficult because they have been analyzed in different host-symbiont systems and transinfection of Wolbachia across different hosts is often challenging. In this study, we demonstrated the effects of nine Wolbachia strains on the splicing of sex-determining genes in Lepidoptera by fixing the host genetic background using a cell culture system. Cell transinfection assays confirmed that three male killing-inducing Wolbachia strains and one feminization-inducing Wolbachia strain increased the female-type splicing products of the core sex-determining genes doublesex, masculinizer, and zinc finger protein 2. Regarding Wolbachia strains that do not induce male killing/feminization, three had no effect on these sex-determining genes, whereas two strains induced female-type splicing of masculinizer and doublesex but not zinc finger protein 2. Comparative genomics confirmed that homologs of oscar, the Wolbachia gene responsible for male killing in Ostrinia, were encoded by male killing/feminizing Wolbachia strains, but not by non-male killing/non-feminizing strains. These results demonstrated the conserved effects underlying male killing and feminization induced by oscar-bearing Wolbachia, and suggested other potential mechanisms that Wolbachia might employ to manipulate host sex. IMPORTANCEArthropods commonly carry maternally transmitted microbial symbionts such as Wolbachia. The lack of paternal transmission frequently led to the evolution of reproductive parasitism traits, namely the manipulation of host reproduction in favor of female hosts, substantiated by male killing and feminization. Although Wolbachia induces these phenotypes in a wide range of insects, the underlying mechanisms, diversity, and commonality remain largely unclear. In this study, we used a combination of transinfection assays and comparative genomics to reveal the conserved effects of male killing and feminizing Wolbachia strains on lepidopteran sex determination. Furthermore, we demonstrated that some non-male killing/non-feminizing Wolbachia strains also have an inherent ability to influence sex determination, albeit in a different manner, suggesting the potential for multiple mechanisms to manipulate host sex. This study also implied the frequent evolution of host suppressors against Wolbachia-induced reproductive manipulation.

microbiology↗

bioRxiv2024

Blood immunophenotyping identifies distinct kidney histopathology and outcomes in patients with lupus nephritis

Lupus nephritis (LN) is a frequent manifestation of systemic lupus erythematosus, and fewer than half of patients achieve complete renal response with standard immunosuppressants. Identifying non-invasive, blood-based pathologic immune alterations associated with renal injury could aid therapeutic decisions. Here, we used mass cytometry immunophenotyping of peripheral blood mononuclear cells in 145 patients with biopsy-proven LN and 40 healthy controls to evaluate the heterogeneity of immune activation in patients with LN and to identify correlates of renal parameters and treatment response. Unbiased analysis identified 3 immunologically distinct groups of patients with LN that were associated with different patterns of histopathology, renal cell infiltrates, urine proteomic profiles, and treatment response at one year. Patients with enriched circulating granzyme B+ T cells at baseline showed more severe disease and increased numbers of activated CD8 T cells in the kidney, yet they had the highest likelihood of treatment response. A second group characterized primarily by a high type I interferon signature had a lower likelihood of response to therapy, while a third group appeared immunologically inactive by immunophenotyping at enrollment but with chronic renal injuries. Main immune profiles could be distilled down to 5 simple cytometric parameters that recapitulate several of the associations, highlighting the potential for blood immune profiling to translate to clinically useful non-invasive metrics to assess immune-mediated disease in LN.

immunology↗

bioRxiv2023

Effects of novelty and temporal distance on post-experience reactivation of hippocampal place cells encoding multiple environments

The hippocampus plays a crucial role in consolidating episodic memories from diverse experiences that encompass spatial, temporal, and novel information. This study analyzed the spike patterns of hippocampal place cells in the CA3 and CA1 areas of rats that sequentially foraged in five rooms, including familiar and novel rooms, followed by a rest period. Across multiple rooms, the generation of place fields by CA1 place cells was coordinated with other place cells. In the subsequent rest period, CA3 place cells that encoded novel environments exhibited stronger and more coordinated reactivation during sharp wave ripples (SWRs) than CA1 place cells. In contrast, CA1 place cells that encoded more recent environments exhibited stronger SWR-associated reactivation, independent of spikes of other cells, with weaker influences from novelty compared to CA3 place cells. These results suggest that post-experience SWR-associated reactivation of CA3 and CA1 neurons primarily processes novelty-related and temporal distance-related aspects of memory, respectively.

neuroscience↗