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Nishida, K.

Publications and source records attributed to Nishida, K..

At least 19 recordsLinked to original sources

SIK3 links synaptic strength to sleep pressure through RhoA signaling

Sleep is regulated by homeostatic sleep pressure, which accumulates during wakefulness, triggering sleep, and dissipates during sleep, leading to wakefulness. Although recent evidence suggests that synaptic potentiation encodes sleep pressure, the intracellular mechanisms linking synaptic strength to sleep pressure remain unclear. Here we demonstrate that the sleep-promoting kinase SIK3 links synaptic strength and sleep pressure through RhoA signalling. We found that SIK3 is required for dendritic spine enlargement induced by chemical long-term potentiation (cLTP) in cultured cortical pyramidal neurons and positively regulates spine size in the prefrontal cortex in vivo. cLTP reduced RhoA activity in an SIK3-dependent manner during spine enlargement, whereas activation of RhoA reduced EEG delta density in vivo during non-rapid eye movement sleep (NREMS), an indicator of sleep pressure. SIK3 substrate screening identified several RhoA regulators including GEF-H1, and further biochemical analyses found that phosphorylation by SIK3 activates GEF-H1. However, contrary to our expectation, RhoA facilitation through pharmacological activation of GEF-H1 enlarged spine size in cultured neurons, and expression of constitutively active GEF-H1 increased NREMS delta density in a RhoA-dependent fashion. Together, these results indicate that SIK3 enlarges spine size and enhances NREMS delta density through two RhoA-dependent pathways, driving mutually opposing intermediate phenotypes. Our findings identify two clashing SIK3-RhoA signalling pathways that couple synaptic regulation to sleep homeostasis.

neuroscience↗

Encapsulated cell technology delivers ciliary neurotrophic factor to promote JAK/STAT-dependent photoreceptor survival in retinal degeneration

Sustained trophic factor delivery via Encapsulated Cell Technology (ECT) is a powerful new class of therapeutics with broad potential for targeted treatment. Intravitreal delivery of ciliary neurotrophic factor (CNTF) via the ECT, NT-501, is a first-in-class therapy that slows the progression of macular telangiectasia type 2 (MacTel). Despite its clinical efficacy, key questions remain regarding its mechanism of action, including whether other implant-derived factors contribute to therapeutic benefit and how optimal dosing should be determined. Resolving these issues is critical for optimizing NT-501 in MacTel and guiding the development of ECT-based therapies for other diseases. We evaluated the biological activity of implant-derived cytokines on retinal tissue, using long-term NT-501 intravitreal implants in rabbits alongside human retinal organoid (hRO) models treated with NT-501-conditioned medium (NT-501-CM). Then, using a MacTel-specific photoreceptor degeneration model in hROs, we showed NT-501-CM significantly reduced photoreceptor cell death, and this protective effect was abolished by either CNTF-neutralizing antibodies or JAK inhibitor. We also established a therapeutic dose-response relationship linking NT-501-derived CNTF levels to JAK/STAT3 activation and photoreceptor protection. These findings directly connect ECT-derived CNTF exposure with JAK/STAT3-mediated photoreceptor protection in human retinal tissue and suggest an optimal concentration range for efficacy.

pharmacology and toxicology↗

MSLipidMapper: a pathway-centered lipidome analysis environment linking lipid class, acyl-chain subsets, and multi-omics data

Lipids exhibit extensive structural diversity arising from variation in lipid classes, subclasses, and acyl-chain compositions, making systematic interpretation of lipidomics data challenging. Although untargeted lipidomics enables the quantification of hundreds to thousands of lipid molecular species, downstream analyses often treat pathway-level summaries, molecular-species visualization, structural subsetting, and multi-omics interpretation as separate steps. Here, we present MSLipidMapper, an R/Shiny-based lipidomics data exploration environment for pathway-centered and structure-aware analysis of annotated lipidomics datasets. MSLipidMapper reconstructs annotated lipid peak tables as Bioconductor SummarizedExperiment objects, thereby organizing quantitative lipid abundance values, sample metadata, lipid subclass annotations, and parsed acyl-chain features within a unified data structure. Lipid molecular species are summarized on static, curated lipid metabolic pathway maps at the subclass level while retaining direct links to the underlying molecular species and acyl-chain annotations. This design enables users to inspect molecular-species patterns underlying each pathway node, define lipid subsets based on structural features such as specific acyl chains, and re-project these subsets onto the same pathway context. Gene or protein expression data can also be overlaid on pathway-associated reactions to support multi-layer interpretation of lipid metabolism. The program is showcased using publicly available aging lipidome datasets of mice, illustrating how subclass-level pathway summaries can be connected to molecular-species heatmaps, acyl-chain-defined subsets, and transcriptome or proteome information.

bioinformatics↗

Genomic characterization of sub-populations in human pluripotent stem cell-derived retinal progenitor cells that drive retinal layer structure

The mechanism underlying retinal spheroid layer formation was investigated using Rax::GFP-positive retinal progenitor cells from human embryonic stem cell-derived retinal organoids. Single-cell RNA sequencing revealed that well-layered spheroids transiently activated canonical WNT2B-FZD7 signaling followed by temporary expression of non-canonical WNT5A. Despite structural differences in vitro, non- layered and well-layered retinal spheroids on differentiation Day 60 successfully developed into cone and rod subtypes of photoreceptors and established synaptic connections with host bipolar cells after transplantation in a retinal degeneration rat model, resulting in light-evoked functional recovery. Additionally, part of the presumable Rax::GFP-positive retinal progenitor cells differentiated into non- retinal lineages, including ciliary marginal zone-like, retinal pigment epithelium, and spinal cord-like tissues in vitro, reflecting the developmental plasticity of RAX-positive cells. These findings suggest that canonical and non-canonical WNT signaling pathways sequentially orchestrate early retinal morphogenesis, whereas environmental factors within the host retina strongly drive the alignment and functional integration of graft photoreceptors.

cell biology↗

A joint probabilistic model of human scene and object recognition via non-hierarchical residual computation

Visual object and scene recognition have been extensively studied, but separately. We here propose that the two processes could be intrinsically linked in the neural system. We developed a Joint Residual Variational Autoencoder (JRVAE) with two networks: VAE1 for coarse scene recognition and VAE2 for object recognition using residuals from VAE1s reconstructions. Our model demonstrates emergent functional specialization when conditioned on information reduction in peripheral vision, with quantitative analysis confirming VAE1 excels at the representation of scenes while VAE2 specializes in that of objects. This architecture naturally implements figure-ground segmentation and aligns with neurobiological evidence of distinct cortical pathways. Our findings suggest residual computation enables joint visual processing that mirrors human perceptions coarse-to-fine principle in perception.

neuroscience↗

Widespread Distribution of α-Synuclein Oligomers in LRRK2-related Parkinson's Disease

Mutations in leucine-rich repeat kinase 2 (LRRK2) are the most common cause of familial and sporadic Parkinsons disease (PD). While the clinical features of LRRK2-PD patients resemble those of typical PD, there are significant differences in the pathological findings. The pathological hallmark of definite PD is the presence of -synuclein (SYN)-positive Lewy-related pathology; however, approximately half of LRRK2-PD cases do not have Lewy-related pathology. Lewy-related pathology is a late-stage SYN aggregation that can be visualized with hematoxylin and eosin stains or conventional immunohistochemistry (IHC). Increasing evidence has indicated that SYN oligomers, which represent the early-stage of SYN aggregation, may have neurotoxicity. Visualization of SYN oligomers requires specialized staining techniques, such as SYN-proximity ligation assay (PLA). The distribution and severity of SYN oligomers in the human brain of LRRK2-PD patients remain unknown. In this study, we performed phosphorylated SYN-IHC and SYN-PLA staining on postmortem brain sections of patients with three pathogenic LRRK2 mutants: p.G2019S (n=5), p.I2020T (n=5), and p.R1441C (n=4). The severity of Lewy-related pathology and SYN oligomers were assessed semi-quantitatively in the brainstem, limbic lobe, basal ganglia, and cerebral cortex. SYN oligomers were detected in LRRK2-PD cases even in cases without Lewy-related pathology; a negative correlation was observed between Lewy-related pathology and SYN oligomers (r=-0.26 [-0.39, -0.12]; P<0.0001). Our findings suggest that SYN oligomers may represent a common pathological feature of LRRK2-PD. Notably, patients harboring p.G2019S and p.I2020T had significantly higher levels of SYN oligomers in those without Lewy-related pathology compared to those with Lewy-related pathology. These cases also had a trend toward shorter disease duration. These results imply that in LRRK2-PD, SYN oligomers may initially accumulate in the brain but do not progress to form Lewy-related pathology. The present study suggests that targeting SYN oligomers may be a therapeutic strategy for LRRK2-PD even if there is no Lewy-related pathology.

neuroscience↗

Development of a highly efficient base editing system for Lactobacilli to improve probiotics and dissect essential functions

Lactobacilli play essential roles in the food industry and are increasingly explored for their potential as probiotics and therapeutic agents. Beneficial strains are primarily isolated from various natural sources including healthy human bodies, and undergo rigorous characterization and safety evaluations. Genomic and genetic information has increasingly accumulated and been linked to their various functions, to which transgenic approaches are being performed to verify crucial genes. In order to reasonably develop more useful strains, beneficial traits need to be introduced into any given strains and enhanced or combined. However, for practical use as probiotics or foods, organisms with transgene are hardly acceptable. Here, we have introduced the base editing Target-AID system specifically for Lactobacilli, enabling precise installation of point mutations without donor DNA and at multiple genomic loci simultaneously. Lactiplantibacillus plantarum has been successfully engineered to reduce production of imidazole propionate, which has been reported to be associated with type 2 diabetes. Additionally, this system enabled transient knock-out of an essential gene, such as one involved in cell division showing severe filamentous cell phenotype, providing a unique approach for dissecting essential gene function. ImportanceThis work provides highly efficient and multiplexable base editing system that installs precise point mutations in the genomes of the two major Lactobacilli strains. As the advanced CRISPR technology so-called non-cleaving genome editing, base editing is less toxic and does not integrate any foreign DNA into the genomes. Our approaches pave the way for dissecting and improving probiotics and food-grade microbes, ultimately creating better human health.

microbiology↗

MS2Lipid: a lipid subclass prediction program using machine learning and curated tandem mass spectral data

Untargeted lipidomics using collision-induced dissociation-based tandem mass spectrometry (CID-MS/MS) is essential for biological and clinical applications. However, annotation confidence is still guaranteed by manual curation by analytical chemists, although various software tools have been developed for automatic spectral processing based on rule-based fragment annotations. In this study, we provide a novel machine learning model, MS2Lipid, for the prediction of lipid subclasses from MS/MS queries to provide an orthogonal decision of lipidomics software programs to determine the lipid subclass of ion features, in which a new descriptor, MCH (mode of carbon and hydrogen), was designed to increase the specificity of lipid subclasses in nominal mass resolution MS data. The model trained with 5,224 and 5,408 manually curated MS/MS spectra for the positive- and negative-ion modes mapped the query into one or several categories of 97 lipid subclasses, with an accuracy of 95.5% queries in the test set. Our program outperformed the CANOPUS ontology prediction program, providing correct annotations for 38.7% of the same test set. The program was further validated using various datasets from different machines and curators, and the average accuracy exceeded 87.4 %. Furthermore, the function of MS2Lipid was showcased by the annotation of novel esterified bile acids, whose abundance was significantly increased in obese patients in a human cohort study, suggesting that the machine learning model provides an independent criterion for lipid subclass classification, in addition to an environment for annotating lipid metabolites that have been previously unknown.

bioinformatics↗

MS-DIAL 5 multimodal mass spectrometry data mining unveils lipidome complexities

Lipidomics and metabolomics communities comprise various informatics tools; however, software programs that can handle multimodal mass spectrometry (MS) data with structural annotations guided by the Lipidomics Standards Initiative are limited. Here, we provide MS-DIAL 5 to facilitate the in-depth structural elucidation of lipids through electron-activated dissociation (EAD)-based tandem MS, as well as determine their molecular localization through MS imaging (MSI) data using a species/tissue-specific lipidome database containing the predicted collision-cross section (CCS) values. With the optimized EAD settings using 14 eV kinetic energy conditions, the program correctly delineated the lipid structures based on EAD-MS/MS data from 96.4% of authentic standards. Our workflow was showcased by annotating the sn- and double-bond positions of eye-specific phosphatidylcholine molecules containing very-long-chain polyunsaturated fatty acids (VLC-PUFAs), characterized as PC n-3-VLC-PUFA/FA. Using MSI data from the eye and HeLa cells supplemented with n-3-VLC-PUFA, we identified glycerol 3-phosphate (G3P) acyltransferase (GPAT) as an enzyme candidate responsible for incorporating n-3 VLC-PUFAs into the sn-1 position of phospholipids in mammalian cells, which was confirmed using recombinant proteins in a cell-free system. Therefore, the MS-DIAL 5 environment, combined with optimized MS data acquisition methods, facilitates a better understanding of lipid structures and their localization, offering novel insights into lipid biology.

bioinformatics↗

Decreased fucosylation impacts epithelial integrity and increases risk for COPD.

COPD causes significant morbidity and mortality worldwide. Epithelial damage is fundamental to disease pathogenesis, although the mechanisms driving disease remain undefined. Published evidence from a COPD cohort (SPIROMICS) and confirmed in a second cohort (COPDgene) demonstrate a polymorphism in Fucosyltransferese-2 (FUT2) is a trans-pQTL for E-cadherin, which is critical in COPD pathogenesis. We found by MALDI-TOF analysis that FUT2 increased terminal fucosylation of E-cadherin. Using atomic force microscopy, we found that FUT2-dependent fucosylation enhanced E-cadherin-E-cadherin bond strength, mediating the improvement in monolayer integrity. Tracheal epithelial cells from Fut2-/- mice have reduced epithelial integrity, which is recovered with reconstitution of Fut2. Overexpression of FUT2 in COPD derived epithelia rescues barrier function. Fut2-/- mice show increased susceptibility in an elastase model of disease developing both emphysema and fibrosis. We propose this is due to the role of FUT2 in proliferation and cell differentiation. Overexpression of FUT2 significantly increased proliferation. Loss of Fut2 results in accumulation of Spc+ cells suggesting a failure of alveolar type 2 cells to undergo transdifferentiation to alveolar type 1. Using a combination of population data, genetically manipulated mouse models, and patient-derived cells, we present a novel mechanism by which post-translational modifications modulate tissue pathology and serve as a proof of concept for the development of a disease-modifying target in COPD.

cell biology↗

LsTT2 encoding R2R3-MYB transcription factor is responsible for a shift from black to white in lettuce seed

Prickly lettuce (Lactuca serriola), which is considered the wild ancestor of lettuce, has black seeds, whereas the major seed color of domesticated lettuce is black or white. The successfully-selected white seed trait is a key domestication trait for lettuce cultivation and breeding; however, the mechanism underlying the shift from black to white seeds remains to be clarified. We aimed to identify the gene/s responsible for white seed trait in lettuce. Genetic mapping of a candidate gene was performed with double-digest RAD sequencing using an F2 population derived from a cross between ShinanoPower (white seed) and Escort (black seed). The white seed trait was controlled by a single recessive locus (48.055-50.197 Mbp) in linkage group 7. Narrowing down using five PCR-based markers and 84 cultivars, eight candidate genes were mapped in the locus. Only the LG7_v8_49.251Mbp_HinfI marker, which employs a single nucleotide mutation in the stop codon of Lsat_1_v5_gn_7_35020.1 was completely linked to the seed color phenotype. In addition, the sequences of the coding region for candidate genes except for Lsat_1_v5_gn_7_35020.1 were identical in the resequence analysis of ShinanoPower (white seed) and Escort (black seed). Therefore, we proposed Lsat_1_v5_gn_7_35020.1, a gene located in the locus, as the candidate gene and designated it as LsTT2, an ortholog encoding the R2R3 MYB transcription factor in Arabidopsis. When we validated the role of LsTT2 in seed color through genome editing, LsTT2 knockout mutants harboring an early termination codon showed a change in seed color from black to white. White seeds accumulated less proanthocyanidins than black seeds, which was similar to the phenotype observed in Arabidopsis TRANSPARENT TESTA 2 (TT2) mutants. Therefore, LsTT2 was the allele responsible for the shift in seed color from black to white. The development of a robust marker for marker-assisted selection and identification of the gene responsible for white seeds has implications for future breeding technology and physiological analysis.

genetics↗

Time-deterministic cryo-optical microscopy

We developed a technique to rapidly freeze biological systems during observation under an optical microscope, which allows for detailed optical observation at a precise time in the biological dynamics at high spatial resolution and quantifiability under low-temperature conditions. Our study further found that ion distributions and molecular conformations can be fixed in space and time, demonstrated by visualization of calcium waves rapid-frozen at an instant using fluorescent ion indicators. These results show that time-deterministic cryo-optical microscopy can suspend cellular dynamics while maintaining molecular and ionic states, allowing us to view cellular dynamics in a way that has not been possible before. One-Sentence SummaryRapid freezing of dynamic biological systems during optical observation presents time information to the fixed samples

biophysics↗

Brn3a controls the soma localization and axonal extension patterns of developing spinal dorsal horn neurons

The spinal dorsal horn comprises heterogeneous neuronal populations, that interconnect with one another to form neural circuits modulating various types of sensory information. Decades of evidence has revealed that transcription factors expressed in each neuronal progenitor subclass play pivotal roles in the cell fate specification of spinal dorsal horn neurons. However, the development of subtypes of these neurons is not fully understood in more detail as yet and warrants the investigation of additional transcription factors. In the present study, we examined the involvement of the POU domain-containing transcription factor Brn3a in the development of spinal dorsal horn neurons. Analyses of Brn3a expression in the developing spinal dorsal horn neurons in mice demonstrated that Brn3a was downregulated in majority of the Brn3a-lineage neurons during embryonic stages (Brn3a-transient neurons), whereas a limited population continued to express Brn3a after E18.5 (Brn3a-persistent neurons). Brn3a knockout disrupted the localization pattern of Brn3a-persistent neurons, indicating a critical role of this transcription factor in the development of these neurons. In contrast, Brn3a overexpression in Brn3a-transient neurons directed their localization in a manner similar to that in Brn3a-persistent neurons. Moreover, Brn3a-overexpressing neurons exhibited increased axonal extension to the ventral and ventrolateral funiculi, where the axonal tracts of Brn3a-persistent neurons reside. These results suggest that Brn3a controls the soma localization and axonal extension patterns of Brn3a-persistent spinal dorsal horn neurons.

neuroscience↗

transomics2cytoscape: An automated software for interpretable 2.5-dimensional visualization of trans-omic networks

Biochemical network visualization is one of the essential technologies for mechanistic interpretation of omics data. In particular, recent advances in multi-omics measurement and analysis require the development of visualization methods that encompass multiple omics data. Visualization in 2.5 dimension (2.5D visualization), which is an isometric view of stacked X-Y planes, is a convenient way to interpret multi-omics/trans-omics data in the context of the conventional layouts of biochemical networks drawn on each of the stacked omics layers. However, 2.5D visualization of trans-omics networks is a state-of-the-art method that primarily relies on time-consuming human efforts involving manual drawing. Here, we present an R Bioconductor package transomics2cytoscape for automated visualization of 2.5D trans-omics networks. We confirmed that transomics2cytoscape could be used for rapid visualization of trans-omics networks presented in published papers within a few minutes. Transomics2cytoscape allows for frequent update/redrawing of trans-omics networks in line with the progress in multi-omics/trans-omics data analysis, thereby enabling network-based interpretation of multi-omics data at each research step. The transomics2cytoscape source code is available at https://github.com/ecell/transomics2cytoscape.

systems biology↗

A multi-kingdom genetic barcoding system for precise target clone isolation

Clonal heterogeneity underlies diverse biological processes, including cancer progression, cell differentiation, and microbial evolution. Cell tagging strategies with DNA barcodes have recently enabled analysis of clone size dynamics and clone-restricted transcriptomic landscapes of heterogeneous populations. However, isolating a target clone that displays a specific phenotype from a complex population remains challenging. Here, we present a new multi-kingdom genetic barcoding system, CloneSelect, in which a target cell clone can be triggered to express a reporter gene for isolation through barcode-specific CRISPR base editing. In CloneSelect, cells are first barcoded and propagated so their subpopulation can be subjected to a given experiment. A clone that shows a phenotype or genotype of interest at a given time can then be isolated from the initial or subsequent cell pools stored throughout the experimental timecourse. This novel CRISPR-barcode genetics platform provides many new ways of analyzing and manipulating mammalian, yeast, and bacterial systems. TeaserA multi-kingdom CRISPR-activatable barcoding system enables the precise isolation of target barcode-labeled clones from a complex cell population.

synthetic biology↗

Involvement of Brn3a-positive spinal dorsal horn neurons in the transmission of visceral pain in inflammatory bowel disease model mice

The spinal dorsal horn (SDH) plays a crucial role in the transmission and processing of somatosensory information. Although spinal neural circuits that process several distinct types of somatic sensations have been studied extensively, those responsible for visceral pain transmission remain poorly understood. In the present study, we analyzed dextran sodium sulfate (DSS)-induced inflammatory bowel disease (IBD) mouse models to characterize the spinal dorsal horn neurons involved in visceral pain transmission. Immunostaining for c-fos, a marker of neuronal activity, demonstrated that numerous c-fos-positive cells were found bilaterally in the lumbosacral spinal dorsal horn, and their distribution was particularly abundant in the shallow dorsal horn. Characterization of these neurons by several molecular markers revealed that the percentage of the Pit1-Oct1-Unc86 domain (POU domain)-containing transcription factor Brn3a-positive neurons among the c-fos-positive neurons in the shallow dorsal horn was 30-40% in DSS-treated mice, which was significantly higher than that in the somatic pain model mice. We further demonstrated by neuronal tracing that, within the shallow dorsal horn, Brn3a-positive neurons were more highly represented in spino-solitary projection neurons than in spino-parabrachial projection neurons. These results raise the possibility that Brn3a-positive spinal dorsal horn neurons make a large contribution to visceral pain transmission, part of which is mediated through the spino-solitary pathway.

neuroscience↗

Knockout of E-cadherin in adult mouse epithelium results in emphysema and airway disease

Chronic obstructive pulmonary disease (COPD) is a devastating lung disease, characterized by a progressive decline in lung function, alveolar loss (emphysema), and airflow limitation due to excessive mucus secretion (chronic bronchitis), that can occur even after the injurious agent is removed. It is slated to rise to the 3rd leading cause of death due to chronic disease by 2030 globally, and the 4th leading cause of death due to chronic disease in the USA. While there is substantial evidence indicating loss of E-cadherin in the lung epithelium of patients with COPD, it is not known if this is causal to the disease. We investigated if loss of E-cadherin can result in lung disease using in both in vitro models of primary, differentiated human cells and in mouse models. Using a cell type-specific promoter using Cre/LoxP mice system to knock-out E- cadherin in ciliated and alveolar epithelial cell (Type 1 and Type 2) populations in adult mouse models, we determined that loss of E-cadherin caused airspace enlargement, as well as increased airway hyperresponsiveness indicating that it does have a causative role in causing COPD. Strategies to upregulate CDH1 (encodes for E-cadherin) in CHBEs and cigarette-smoke injured NHBEs can rescue the dysfunctional epithelium.

cell biology↗

Histone H3K4me3 and H3K9me3 are super over-methylated in soft tissue sarcoma compared to normal muscle in patient-derived xenograft (PDX) mouse models: an indicator of cancer methionine addiction

Methionine addiction is a fundamental and general hallmark of cancer discovered by us almost a half-century ago [Proc Natl Acad Sci U S A 73 (1976) 1523-1527]. Methionine addiction is defined as the requirement, specific for cancer cells of all types, for exogenous methionine despite the normal ability to synthesize methionine from homocysteine. The methionine addiction of cancer is termed the Hoffman-effect, analogous to the Warburg-effect of the high glucose requirement of cancer cells. Methionine addiction is due to excess transmethylation reactions resulting in high methionine flux in cancer cells, which causes them to selectively arrest under methionine restriction due to depletion of free methionine and S-adenosyl methionine. Recently we have shown methionine-addicted cancer cells over-methylate histone H3 lysine marks which are not over-methylated in normal cells or in low-malignancy methionine-independent revertants derived from methionine-addicted cancer cells. In the present report, we show that in patient-derived xenograft (PDX) mouse models of the most common soft tissue sarcomas: myxofibrosarcoma, undifferentiated pleomorphic sarcoma (UPS) and liposarcoma, histone H3K4me3 and H3K9me3 are super over-methylated compared to normal muscle tissue. This new result is discussed along with our previous reports, regarding the potential of histone H3 over-methylation as a basis of malignancy.

cancer biology↗