Biology subjects

Matsumoto, S.

Publications and source records attributed to Matsumoto, S..

29 records · Page 2Linked to original sources

bioRxiv2022

Aberrant association of chromatin with nuclear periphery induced by Rif1 leads to mitotic defect and cell death.

Chromatin is compartmentalized in nuclei and its architecture and nuclear location may have impacts on chromatin events. Rif1, identified as a potent suppressor of hsk1-null mutation (defective in initiation of DNA replication) in fission yeast, recognizes G-quadruplex structures and inhibits origin firing in their 50[~]100-kb vicinity, leading us to postulate that Rif1 may generate chromatin higher-order structures inhibitory for initiation. However, effects of Rif1 on chromatin localization in nuclei have not been known. We show here that overexpression of Rif1 causes growth inhibition and eventually cell death in fission yeast. Chromatin binding activities of Rif1, but not recruitment of phosphatase PP1, are required for growth inhibitory effect. Overexpression of a PP1 binding site mutant of Rif1 does not delay S-phase, but still causes cell death, indicating that cell death is caused not by S-phase problems but by issues in other phases of cell cycle, most likely M-phase. Indeed, Rif1 overexpression generates cells with unequally segregated chromosomes. Rif1 overexpression relocates chromatin near nuclear periphery in a manner dependent on its chromatin-binding ability, and this correlates with growth inhibition and cell death induction. Thus, regulated Rif1-mediated chromatin association with nuclear periphery is important for coordinated progression of S- and M-phases.

molecular biology↗

bioRxiv2022

Pelagic seabirds reduce risk by flying into the eye of the storm

Cyclones can cause mass mortality of seabirds, sometimes wrecking thousands of individuals. The few studies to track pelagic seabirds during cyclones show they tend to circumnavigate the strongest winds. We tracked adult shearwaters in the Sea of Japan over 11 years and find that the response to cyclones varied according to the wind speed and direction. In strong winds, birds that were sandwiched between the storm and mainland Japan flew away from land and towards the eye of the storm, flying within [≤] 30 km of the eye and tracking it for up to 8 hours. This exposed shearwaters to some of the highest wind speeds near the eye wall ([≤] 21 m s-1), but enabled them to avoid strong onshore winds in the storms wake. Extreme winds may therefore become a threat when an inability to compensate for drift could lead to forced landings and collisions. Birds may need to know where land is in order to avoid it. This provides additional selective pressure for a map sense and could explain why juvenile shearwaters, which lack a map sense, instead navigating using a compass heading, are susceptible to being wrecked. We suggest that the ability to respond to storms is influenced by both flight and navigational capacities. This may become increasingly pertinent due to changes in extreme weather patterns. Significance StatementCyclones can cause billions of dollars of damage and loss of human life. They can also cause mass mortality and strandings in seabirds. We used GPS tracking data from streaked shearwaters breeding in the worlds most active cyclone basin to understand how seabirds respond to these systems. Birds varied their response according to the wind speed and direction, generally flying towards the eye of the cyclone in strong winds. This surprising strategy enables dynamic soaring birds to control their exposure to risky wind vectors that could drift them onshore. Nonetheless, birds may need to know where land is in order to avoid it. Juveniles lack this "map sense", making them susceptible to wrecking in some scenarios.

ecology↗

bioRxiv2021

Intracellular force comparison of pathogenic KIF1A, KIF5, and dynein by fluctuation analysis

In mammalian cells, there exist approximately 40 types of microtubule motor proteins that are assigned to specific cargo deliveries. For example, the kinesin-1 family motor KIF5 is the major motor responsible for anterograde mitochondrial transport, whereas the kinesin-3 family motor KIF1A is responsible for synaptic vesicle precursor transport. In contrast, cytoplasmic dynein is responsible for retrograde transport of nearly all cargos. The force and velocity of these microtubule motors have been investigated in in-vitro single-molecule experiments. In the present study, we compared the intracellular force and velocity of various types of motors in the mammalian neuronal axon obtained by non-invasive force measurement (fluctuation analysis) and extreme value analysis with those obtained by previous single-molecule experiments. As we found a high correlation between our results and the previous results, we next investigated synaptic vesicle precursor transport by hereditary spastic paraplegia-associated KIF1A variants (V8M, R350G, and A255V). KIF1A-V8M and KIF1A-A255V exhibited force and velocity impairment in mammalian neuronal axons, whereas the physical property of KIF1A-R350G was similar to that of the wild type. We believe that the development of new analytical techniques for investigating intracellular cargo transports is helpful to elucidate the molecular mechanism of KIF1A-associated neurological disorders. Statement of SignificanceRecent in-vitro single-molecule experiments have clearly revealed that microtubule motors only fully exert their functions when fully equipped with the proteins associated with cargo vesicle transport. This emphasizes the significance of intracellular physical measurements, in which the motors should fully function. In addition to motor force and velocity, the number of motors transporting a single cargo together is an important physical quantity to characterize cargo transport, but is difficult to estimate using in-vitro single-molecule experiments. In this study, we aimed to extract physical information on microtubule motors in the intracellular environment.

biophysics↗

bioRxiv2021

SARS-CoV-2 infection studies in lung organoids identify TSPAN8 as novel mediator

SARS coronavirus-2 (SARS-CoV-2) is causing a global pandemic with large variation in COVID-19 disease spectrum. SARS-CoV-2 infection requires host receptor ACE2 on lung epithelium, but epithelial underpinnings of variation are largely unknown. We capitalized on comprehensive organoid assays to report remarkable variation in SARS-CoV-2 infection rates of lung organoids from different subjects. Tropism is highest for TUBA- and MUC5AC-positive organoid cells, but levels of TUBA-, MUC5A-, or ACE2-positive cells do not predict infection rate. We identify surface molecule Tetraspanin 8 (TSPAN8) as novel mediator of SARS-CoV-2 infection, which is not downregulated by this specific virus. TSPAN8 levels, prior to infection, strongly correlate with infection rate and TSPAN8-blocking antibodies diminish SARS-CoV-2 infection. We propose TSPAN8 as novel functional biomarker and potential therapeutic target for COVID-19.

microbiology↗

bioRxiv2021

Recruitment of KRAS downstream target ARL4C to membrane protrusions accelerates pancreatic cancer cell invasion.

Pancreatic cancer (PC) has a high mortality rate due to metastasis. Whereas KRAS is mutated in most PC patients, controlling KRAS or its downstream effectors has not been succeeded clinically. ARL4C is a small G protein whose expression is induced by the Wnt and EGF-RAS pathways. In the present study, we found that ARL4C is frequently overexpressed in PC patients and showed that its unique localization to membrane protrusions is required for cancer cell invasion. IQGAP1 was identified as a novel interacting protein for ARL4C. ARL4C recruited IQGAP1 and its downstream effector, MMP14, to membrane protrusions. Specific localization of ARL4C, IQGAP1, and MMP14 was the active site of invasion, which induced degradation of the extracellular matrix. Moreover, subcutaneously injected antisense oligonucleotide (ASO) against ARL4C into tumor-bearing mice suppressed metastasis of PC. These results suggest that ARL4C-IQGAP1-MMP14 signaling is activated at membrane protrusions of PC cells.

cancer biology↗

bioRxiv2020

Exploring ligand binding pathways on proteins using hypersound-accelerated molecular dynamics

Capturing the dynamic processes of biomolecular systems in atomistic detail remains difficult despite recent experimental advances. Although molecular dynamics (MD) techniques enable atomic-level observations, simulations of "slow" biomolecular processes (with timescales longer than submilliseconds) are challenging, due to current computer speed limitations. Therefore, we developed a new method to accelerate MD simulations by high-frequency ultrasound perturbation. The binding events between the protein CDK2 and its small-molecule inhibitors were nearly undetectable in 100-ns conventional MD, but the new method successfully accelerated their slow binding rates by up to 10-20 times. The accelerated MD simulations revealed a variety of microscopic kinetic features of the inhibitors on the protein surface, such as the existence of different binding pathways to the active site. Moreover, the simulations allowed estimating the corresponding kinetic parameters and exploring other druggable pockets. This method can thus provide deeper insight into the microscopic interactions controlling biomolecular processes.

biophysics↗

bioRxiv2020

Inhibition of KDM1A activity restores adult neurogenesis and improves hippocampal memory in a mouse model of Kabuki syndrome

Kabuki syndrome (KS) is a rare cause of intellectual disability primarily caused by loss of function mutations in lysine-specific methyltransferase 2D (KMT2D), which normally adds methyl marks to lysine 4 on histone 3. Previous studies have shown that a mouse model of KS (Kmt2d+/{beta}Geo) demonstrates disruption of adult neurogenesis and hippocampal memory. Proof-of-principle studies have shown postnatal rescue of neurological dysfunction following treatments that promote chromatin opening, however, these strategies are non-specific and do not directly address the primary defect of histone methylation. Since lysine-specific demethylase 1A (LSD1/KDM1A) normally removes the H3K4 methyl marks added by KMT2D, we hypothesize that inhibition of KDM1A demethylase activity may ameliorate molecular and phenotypic defects stemming from KMT2D loss. To test this hypothesis, we evaluated a recently developed KDM1A inhibitor (TAK-418) in Kmt2d+/{beta}Geo mice. We find that orally administered TAK-418 increases the numbers of newly born Doublecortin (DCX)+ cells and processes in hippocampus in a dose dependent manner. We also observe TAK-418-dependent rescue of histone modification defects in hippocampus both by Western blot and ChIP-Seq. Treatment rescues gene expression abnormalities including those of immediate early genes such as FBJ osteosarcoma oncogene (Fos) and FBJ osteosarcoma oncogene homolog B (Fosb). After 2 weeks of TAK-418, Kmt2d+/{beta}Geo mice demonstrate normalization of hippocampal memory defects. In summary, our data suggest that KDM1A inhibition is a plausible treatment strategy for KS and support the hypothesis that the epigenetic dysregulation secondary to KMT2D dysfunction plays a major role in the postnatal neurological disease phenotype in KS.

genetics↗

bioRxiv2020

Extraction of Protein Dynamics Information Hidden in Cryo-EM Map Using Deep Learning

Technical breakthroughs in cryogenic electron microscopy (cryo-EM)-based single-particle analysis have enabled the structures of numerous proteins to be solved at atomic or near-atomic resolutions, including extremely large macromolecules whose structures could not be solved by conventional techniques. Determining the dynamics properties of these macromolecules, based on their solved structures, can further improve our understanding of their functional mechanisms. However, such analysis is often hampered by the large molecular size and complex structural assembly, making both experimental and computational approaches to determine dynamics properties challenging. Here, we report a deep learning-based approach, DEFMap, to extract the dynamics information "hidden" in cryo-EM density maps. By relying only on cryo-EM maps, DEFMap successfully provided dynamics information equivalent to that determined from molecular dynamics (MD) simulations and experimental approaches at the atomic and residue levels. Additionally, DEFMap could detect dynamics changes associated with molecular recognition and the accompanying allosteric conformational stabilizations, which trigger various biological events such as signal transduction and enzyme catalysis. This approach will provide new insights into the functional mechanisms of biological molecules, accelerating modern molecular biology researches. Furthermore, this advanced strategy combining experimental data, deep learning approaches, and MD simulations would open a new multidisciplinary science area

molecular biology↗

bioRxiv2019

AI on animals: AI-assisted animal-borne logger never misses the moments that biologists want

Animal-borne data loggers, i.e., biologgers, allow researchers to record a variety of sensor data from animals in their natural environments (Hussey et al. 2015; Kays et al. 2015). This data allows biologists to observe many aspects of the animals lives, including their behavior, physiology, social interactions, and external environment. However, the need to limit the size of these devices to a small fraction of the animals size imposes strict limits on the devices hardware and battery capacities (Kays et al. 2015). Here we show how AI can be leveraged on board these devices to intelligently control their activation of costly sensors, e.g., video cameras, allowing them to make the most of their limited resources during long deployment periods. Our method goes beyond previous works that have proposed controlling such costly sensors using simple threshold-based triggers, e.g., depth-based (Watanuki et al. 2007; Volpov et al. 2015) and acceleration-based (Nishiumi et al. 2018; Brown et al. 2012) triggers. Using AI-assisted biologgers, biologists can focus their data collection on specific complex target behaviors such as foraging activities, allowing them to automatically record video that captures only the moments they want to see. By doing so, the biologger can reserve its battery power for recording only those target activities. We anticipate our work will provide motivation for more widespread adoption of AI techniques on biologgers, both for intelligent sensor control and intelligent onboard data processing. Such techniques can not only be used to control what is collected by such devices, but also what is transmitted off the devices, such as is done by satellite relay tags (Cox et al. 2018).

ecology↗

bioRxiv2019

Characterization and function of medium and large extracellular vesicles from plasma and urine by surface antigens and Annexin V

Medium/large extracellular vesicles (m/lEVs) are released by most cell types and are involved in multiple basic biological processes. Analysis of m/lEV levels in blood or urine may help unravel pathophysiological findings in many diseases. However, it remains unclear how many naturally-occurring m/lEV subtypes exist as well as how their characteristics and functions differ from one another. Here, we identified m/lEVs pelleted from plasma and urine samples by differential centrifugation and showed by flow cytometry that they typically possessed diameters between 200 nm and 800 nm. Using proteomic profiling, we identified several proteins involved in m/lEV biogenesis including adhesion molecules, peptidases and exocytosis regulatory proteins. In healthy human plasma, we could distinguish m/lEVs derived from platelets, erythrocytes, monocytes/macrophages, T and B cells, and vascular endothelial cells using various surface antigens. m/lEVs derived from erythrocytes and monocytes were Annexin V positive. In urine, 50% of m/lEVs were Annexin V negative but contained various membrane peptidases derived from renal tubular villi. Urinary m/lEVs, but not plasma m/lEVs, showed peptidase activity. The method we have developed to characterize cell-derived m/lEVs suggests the possibility of clinical applications.

molecular biology↗

bioRxiv2019

Distinguishing Closely Related Pancreatic Cancer Subtypes In Vivo by 13C Glucose MRI without Hyperpolarization

Metabolic differences between patients and within the tumor itself can be an important determinant in cancer treatment outcome. However, methods for determining these differences non-invasively in vivo have been lacking. Using pancreatic ductal adenocarcinoma as a model, we demonstrate that tumor xenografts with a similar genetic background can be distinguished by their differing rates of metabolism, as detected by imaging of uniformly 13C labeled glucose tracers using a newly developed technique using tensor decomposition for noise suppression to bring the signal to a detectable level without hyperpolarization of the tracer. Using this method, cancer subtypes that appeared to exhibit similar metabolic profiles by other techniques that measured steady state metabolism can be distinguished.

cancer biology↗