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"Nakamura, Takumi"
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The molecular pathology of schizophrenia: an overview of existing knowledge and new directions for future research
2023
Despite enormous efforts employing various approaches, the molecular pathology in the schizophrenia brain remains elusive. On the other hand, the knowledge of the association between the disease risk and changes in the DNA sequences, in other words, our understanding of the genetic pathology of schizophrenia, has dramatically improved over the past two decades. As the consequence, now we can explain more than 20% of the liability to schizophrenia by considering all analyzable common genetic variants including those with weak or no statistically significant association. Also, a large-scale exome sequencing study identified single genes whose rare mutations substantially increase the risk for schizophrenia, of which six genes (
SETD1A
,
CUL1
,
XPO7
,
GRIA3
,
GRIN2A
, and
RB1CC1
) showed odds ratios larger than ten. Based on these findings together with the preceding discovery of copy number variants (CNVs) with similarly large effect sizes, multiple disease models with high etiological validity have been generated and analyzed. Studies of the brains of these models, as well as transcriptomic and epigenomic analyses of patient postmortem tissues, have provided new insights into the molecular pathology of schizophrenia. In this review, we overview the current knowledge acquired from these studies, their limitations, and directions for future research that may redefine schizophrenia based on biological alterations in the responsible organ rather than operationalized criteria.
Journal Article
Transcriptomic dysregulation and autistic-like behaviors in Kmt2c haploinsufficient mice rescued by an LSD1 inhibitor
2024
Recent studies have consistently demonstrated that the regulation of chromatin and gene transcription plays a pivotal role in the pathogenesis of neurodevelopmental disorders. Among many genes involved in these pathways,
KMT2C
, encoding one of the six known histone H3 lysine 4 (H3K4) methyltransferases in humans and rodents, was identified as a gene whose heterozygous loss-of-function variants are causally associated with autism spectrum disorder (ASD) and the Kleefstra syndrome phenotypic spectrum. However, little is known about how
KMT2C
haploinsufficiency causes neurodevelopmental deficits and how these conditions can be treated. To address this, we developed and analyzed genetically engineered mice with a heterozygous frameshift mutation of
Kmt2c
(
Kmt2c
+/fs
mice) as a disease model with high etiological validity. In a series of behavioral analyses, the mutant mice exhibit autistic-like behaviors such as impairments in sociality, flexibility, and working memory, demonstrating their face validity as an ASD model. To investigate the molecular basis of the observed abnormalities, we performed a transcriptomic analysis of their bulk adult brains and found that ASD risk genes were specifically enriched in the upregulated differentially expressed genes (DEGs), whereas KMT2C peaks detected by ChIP-seq were significantly co-localized with the downregulated genes, suggesting an important role of putative indirect effects of
Kmt2c
haploinsufficiency. We further performed single-cell RNA sequencing of newborn mouse brains to obtain cell type-resolved insights at an earlier stage. By integrating findings from ASD exome sequencing, genome-wide association, and postmortem brain studies to characterize DEGs in each cell cluster, we found strong ASD-associated transcriptomic changes in radial glia and immature neurons with no obvious bias toward upregulated or downregulated DEGs. On the other hand, there was no significant gross change in the cellular composition. Lastly, we explored potential therapeutic agents and demonstrate that vafidemstat, a lysine-specific histone demethylase 1 (LSD1) inhibitor that was effective in other models of neuropsychiatric/neurodevelopmental disorders, ameliorates impairments in sociality but not working memory in adult
Kmt2c
+/fs
mice. Intriguingly, the administration of vafidemstat was shown to alter the vast majority of DEGs in the direction to normalize the transcriptomic abnormalities in the mutant mice (94.3 and 82.5% of the significant upregulated and downregulated DEGs, respectively,
P
< 2.2 × 10
−16
, binomial test), which could be the molecular mechanism underlying the behavioral rescuing. In summary, our study expands the repertoire of ASD models with high etiological and face validity, elucidates the cell-type resolved molecular alterations due to
Kmt2c
haploinsufficiency, and demonstrates the efficacy of an LSD1 inhibitor that might be generalizable to multiple categories of psychiatric disorders along with a better understanding of its presumed mechanisms of action.
Journal Article
GWAS-identified bipolar disorder risk allele in the FADS1/2 gene region links mood episodes and unsaturated fatty acid metabolism in mutant mice
by
Lee-Okada, Hyeon-Cheol
,
Takata, Atsushi
,
Yokomizo, Takehiko
in
631/378
,
64/60
,
692/699/476/1333
2023
Large-scale genome-wide association studies (GWASs) on bipolar disorder (BD) have implicated the involvement of the fatty acid desaturase (
FADS
) locus. These enzymes (FADS1 and FADS2) are involved in the metabolism of eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA), which are thought to potentially benefit patients with mood disorders. To model reductions in the activity of FADS1/2 affected by the susceptibility alleles, we generated mutant mice heterozygously lacking both
Fads1
/
2
genes. We measured wheel-running activity over six months and observed bipolar swings in activity, including hyperactivity and hypoactivity. The hyperactivity episodes, in which activity was far above the norm, usually lasted half a day; mice manifested significantly shorter immobility times on the behavioral despair test performed during these episodes. The hypoactivity episodes, which lasted for several weeks, were accompanied by abnormal circadian rhythms and a marked decrease in wheel running, a spontaneous behavior associated with motivation and reward systems. We comprehensively examined lipid composition in the brain and found that levels of certain lipids were significantly altered between wild-type and the heterozygous mutant mice, but no changes were consistent with both sexes and either DHA or EPA was not altered. However, supplementation with DHA or a mixture of DHA and EPA prevented these episodic behavioral changes. Here we propose that heterozygous
Fads1
/
2
knockout mice are a model of BD with robust constitutive, face, and predictive validity, as administration of the mood stabilizer lithium was also effective. This GWAS-based model helps to clarify how lipids and their metabolisms are involved in the pathogenesis and treatment of BD.
Journal Article
Amplitude control of self-excited weakly coupled cantilevers for mass sensing using nonlinear velocity feedback control
by
Yano, Masatoshi
,
Yabuno, Hiroshi
,
Nakamura, Takumi
in
Amplitudes
,
Automotive Engineering
,
Classical Mechanics
2020
Self-excited weakly coupled resonators are an effective way to measure a small biochemical mass in a liquid environment because such resonators can compensate for the viscosity of a measurement environment and have higher sensitivity than previous methods. Self-excitation causes the mode to change from linear to nonlinear dynamics accompanied by larger amplitudes. To prevent this deviation, an amplitude control method using the nonlinearity present in the systems is proposed for various systems. The amplitude control method for self-excited weakly coupled cantilevers has been used experimentally, but its theoretical validity has not been investigated. In the present study, we propose a nonlinear feedback method to control the amplitudes of self-excited weakly coupled cantilevers. Nontrivial steady-state amplitude control is achieved in the first mode. The relationship between the nonlinear feedback gain and the amplitudes is revealed. The validity of the proposed method is confirmed by conducting an amplitude control experiment using weakly coupled microcantilevers. These results raise the possibility of small-mass sensing using self-excited weakly coupled cantilevers in highly viscous environments.
Journal Article
Investigation for Factors Affecting Body Perception Disturbance in Patients with Low Back Pain by Mechanism-Based Classification of Pain: A Cross-Sectional Study
2023
Background. Central sensitization is a pathophysiological cause of chronic low back pain and is linked with psychosocial factors. The association between central sensitization (CS) and body perception disturbance is currently unclear, and no prior studies have investigated this relationship in patients with acute or subacute low back pain. The objective of this study was to investigate potential factors that influence body perception disturbance using a mechanistic classification of low back pain. Methods. This cross-sectional study was conducted at the time of initial physical therapy in patients with low back pain. During the study period, 169 patients were recruited. Pain intensity, disease duration, disability, CS, and body perception disturbance were evaluated. Patients were divided into three groups according to the pathology of low back pain, and multivariate analysis was used to examine factors affecting body perception disturbance. The dependent variable was Fremantle Back Awareness Questionnaire (FreBAQ); the independent variables were age, gender, BMI, VAS, disease duration, RDQ, and CS Inventory-9 (CSI-9). Results. A total of 117 patients were included in our analysis. According to the mechanistic classification of pain, 66 (56.4%), 36 (30.8%), and 15 (12.8%) patients were categorized as having nociceptive pain (NP), peripheral neuropathic pain (PNP), and CS pain (CSP), respectively. Patients with PNP or CSP were significantly older than those with NP p < 0.01. FreBAQ and RDQ scores were significantly higher in patients with CSP than those with NP p < 0.05. The results of multiple regression analyses indicated that CSI-9 scores were significantly associated with FreBAQ p < 0.01. Conclusion. Patients with CS syndrome and low back pain tend to have higher CSI-9 scores and be older. Body perception disturbance is influenced by CS or CS syndrome, regardless of the stage of low back pain, suggesting that patients with chronic low back pain tend to have low body image.
Journal Article
Cryptococcus gattii alters immunostimulatory potential in response to the environment
2019
Cryptococcus gattii is a capsular fungal pathogen, which causes life-threatening cryptococcosis in immunocompetent individuals. This emerging pathogen is less likely to be recognized by innate immunity compared to traditional Cryptococcus neoformans strains. Previous studies indicate that C-type lectin receptors (CLRs), including dectin-1 and dectin-2, play a role in recognizing cryptococcal cells; however, it remains to be elucidated whether the receptors physically associate with C. gattii yeast cell surfaces. Based on the previous findings, we hypothesized that culture conditions influence the expression or exposure of CLR ligands on C. gattii. Therefore, in the present study, we first investigated the culture conditions that induce exposure of CLR ligands on C. gattii yeast cells via the binding assay using recombinant fusion proteins of mouse CLR and IgG Fc, Fc dectin-1 and Fc dectin-2. Common fungal culture media, such as yeast extract-peptone-dextrose (YPD) broth, Sabouraud broth, and potato dextrose agar, did not induce the exposure of dectin-1 ligands, including β-1,3-glucan, on both capsular and acapsular C. gattii strains, in contrast to Fc dectin-1 and Fc dectin-2 bound to C. gattii cells growing in the conventional synthetic dextrose (SD) medium [may also be referred to as a yeast nitrogen base with glucose medium]. The medium also induced the exposure of dectin-1 ligands on C. neoformans, whereas all tested media induced dectin-1 and dectin-2 ligands in a control fungus Candida albicans. Notably, C. gattii did not expose dectin-1 ligands in SD medium supplemented with yeast extract or neutral buffer. In addition, compared to YPD medium-induced C. gattii, SD medium-induced C. gattii more efficiently induced the phosphorylation of Syk, Akt, and Erk1/2 in murine dendritic cells (DCs). Afterwards, the cells were considerably engulfed by DCs and remarkably induced DCs to secrete the inflammatory cytokines. Overall, the findings suggest that C. gattii alters its immunostimulatory potential in response to the environment.
Journal Article
Systematic analysis of exonic germline and postzygotic de novo mutations in bipolar disorder
2021
Bipolar disorder is a severe mental illness characterized by recurrent manic and depressive episodes. To better understand its genetic architecture, we analyze ultra-rare de novo mutations in 354 trios with bipolar disorder. For germline de novo mutations, we find significant enrichment of loss-of-function mutations in constrained genes (corrected-
P
= 0.0410) and deleterious mutations in presynaptic active zone genes (FDR = 0.0415). An analysis integrating single-cell RNA-sequencing data identifies a subset of excitatory neurons preferentially expressing the genes hit by deleterious mutations, which are also characterized by high expression of developmental disorder genes. In the analysis of postzygotic mutations, we observe significant enrichment of deleterious ones in developmental disorder genes (
P
= 0.00135), including the
SRCAP
gene mutated in two unrelated probands. These data collectively indicate the contributions of both germline and postzygotic mutations to the risk of bipolar disorder, supporting the hypothesis that postzygotic mutations of developmental disorder genes may contribute to bipolar disorder.
The significance of rare and de novo variants in bipolar disorder is not well understood. Here, the authors have analyzed whole exome/genome data from trios to identify deleterious de novo variants associated with bipolar disorder.
Journal Article
Attrition‐Enhanced Asymmetric Transformation of Axially Chiral Nicotinamides by Dynamic Chiral Salt Formation
by
Ban, Kazuma
,
Nakamura, Takumi
,
Ishikawa, Hiroki
in
asymmetric amplification
,
axial chirality
,
chiral salt
2022
Atroposelective resolution for axially chiral nicotinamides was achieved by dynamic chiral salt formation with L‐DBTA using six types of nicotinamides that could not be optically resolved by the preferential crystallization method. Kinetic studies of their racemization indicated that the chiral conformation was retained for a significant period of time. Two methods of crystallization‐induced asymmetric transformation were examined by dynamic diastereomeric salt formation: solvent evaporation from a supersaturated solution, and attrition‐enhanced asymmetric transformation. The attrition method was more effective for asymmetric amplification of diastereomeric salts of axially chiral materials. Attrition of equimolar amount of the nicotinamide salts with L‐DBTA converged to one diastereomer salts, and the corresponding enantiomers in 87–99 % ee were obtained after the chiral acid was removed. Changing the ratio of two of the nicotinamides with L‐DBTA to 1 : 2 inverted the axial chirality. Attrition‐enhanced asymmetric transformation of six axially chiral nicotinamides was performed by dynamic chiral salt formation with L‐DBTA. Dynamic crystallization with epimerization of equimolar amounts of nicotinamide salts and L‐DBTA converged to the (−)‐enantiomer with 87–99 % ee. Changing the ratio of two of the nicotinamides with L‐DBTA to 1 : 2 inverted the axial chirality.
Journal Article
Mechanism of sensory perception unveiled by simultaneous measurement of membrane voltage and intracellular calcium
2024
Measuring neuronal activity is important for understanding neuronal function. Ca
2+
imaging by genetically encoded calcium indicators (GECIs) is a powerful way to measure neuronal activity. Although it revealed important aspects of neuronal function, measuring the neuronal membrane voltage is important to understand neuronal function as it triggers neuronal activation. Recent progress of genetically encoded voltage indicators (GEVIs) enabled us fast and precise measurements of neuronal membrane voltage. To clarify the relation of the membrane voltage and intracellular Ca
2+
, we analyzed neuronal activities of olfactory neuron AWA in
Caenorhabditis elegans
by GCaMP6f (GECI) and paQuasAr3 (GEVI) responding to odorants. We found that the membrane voltage encodes the stimuli change by the timing and the duration by the weak semi-stable depolarization. However, the change of the intracellular Ca
2+
encodes the strength of the stimuli. Furthermore, ODR-3, a G-protein alpha subunit, was shown to be important for stabilizing the membrane voltage. These results suggest that the combination of calcium and voltage imaging provides a deeper understanding of the information in neural circuits.
Simultaneous imaging of intracellular Ca
2+
and membrane voltage in olfactory neurons in C. elegans revealed that the membrane voltage encoded the presence of stimuli and the onset of an appropriate concentration of odor stimulus.
Journal Article
Quantitative evaluation of incomplete preweaning lethality in mice by using the CRISPR/Cas9 system
2018
Various molecular biology techniques implementing genome editing have made it possible to generate mouse mutants for nearly all known genes; as a result, the International Mouse Phenotyping Consortium (IMPC) database listing the phenotypes of genetically modified mice has been established. Among mouse phenotypes, lethality is crucial to evaluate the importance of genes in mouse survival. Although many genes are reported to show “preweaning lethality, incomplete penetrance” in the IMPC database, the survival rates of homozygous knockout mice are highly variable. Here, we propose the lethal allele index (LAI), the ratio of the observed number of mice with homozygous knockout (KO) to the theoretically predicted number of homozygous KO mice, as a simple quantitative indicator of preweaning lethality. Among the mice mutants registered as incompletely lethal in IMPC, the LAI calculated from the genotypes of F
1
mice tended to be lower in disease-related genes, and correlated with the frequency of loss-of-function (LOF) alleles in humans. In genome-edited mice using CRISPR/Cas9, the number of mice with homozygous frameshift alleles seemed to be associated with lethality. We edited the
Ehd1
gene in cell lines as well as mice using CRISPR/Cas9, and found that the genotype distribution was significantly different. The LAI calculated from these data was similar to the value calculated from the IMPC data. These findings support the potential usefulness of the LAI as an index of preweaning lethality in genome-edited mice.
Journal Article