Biology subjects

Kikuchi, M.

Publications and source records attributed to Kikuchi, M..

18 recordsLinked to original sources

bioRxiv2026

Multi-modal ion-transport function of potassium channelrhodopsins

Light-gated K+ channelrhodopsins (KCRs) are recognized as an ideal neuronal silencing tool in optogenetics. KCRs contain functionally important residues for a light-driven H+ pump bacteriorhodopsin, but their roles have been unclear. Utilizing electrophysiological methods, we demonstrate that KCRs function as a light-driven H+ pump in the absence of K+. Transport experiments using pH electrodes further elucidated the function of the H+-pump, which operates even in the presence of K+. The hypothesis that the H+ pump exerts a blocking effect on K+ transport in KCRs has been postulated. Furthermore, we ascertained that there was conversion of KCRs from the H+ pump into the H+ channel by light, yet this conversion was never reversed. However, the addition of K+ resulted in the formation of the K+ channel. KCRs exhibit three distinct functional states, H+ pump, H+ channel, and K+ channel. These multifaceted functions are modulated by environmental ions and light.

biophysics↗

bioRxiv2026

Whole-genome duplication underlies conserved sexually biased expression of meiotic cohesin genes unique to the teleost fish lineage

Meiosis is a fundamental process in producing both sperm and eggs, yet recombination landscapes often exhibit sexual differences, known as heterochiasmy. Since meiotic proteins are generally expressed in both sexes, the molecular mechanism driving heterochiasmy remains elusive. The -kleisin subunit gene of meiotic cohesin, Rec8, is expressed bisexually in mammals, while its putative teleost ortholog, rec8a, is expressed in a female-biased manner, presumably due to the presence of its paralog originating from the teleost-specific whole-genome duplication (TGD). Here, we elucidated the evolutionary history and expression dynamics of -kleisin genes across teleost lineages. Through comprehensive phylogenetic and synteny analyses, we revealed that major teleost lineages retain two copies of rec8 and rad21, with rec8 loci experiencing drastic chromosomal rearrangements immediately after the TGD. Using in situ hybridization and single-cell transcriptome data in medaka and zebrafish, we demonstrated a conserved sexually biased expression pattern: rec8a is predominantly female-biased, whereas rec8b exhibits male-biased expression during gametogenesis. Furthermore, comparative epigenetic analyses revealed that the conserved sexually biased expression is driven by lineage-specific cis-regulatory elements, rather than conserved ones. Motif analyses imply that regulatory rewiring by transcription factors, including foxl2l in particular, might have played a crucial role in the establishment and maintenance of this paralog divergence. Our findings highlight how whole-genome duplication and subsequent genomic and epigenetic rewiring subdivided the bisexual function of rec8, offering insights into sexually distinct meiotic regulation. HighlightsO_LITeleosts possess a unique -kleisin repertoire originating from the TGD. C_LIO_LITeleost rec8 paralogs exhibit conserved sex-biased expression during meiosis. C_LIO_LIDrastic genomic rearrangements after the duplication rewired the teleost rec8 loci. C_LIO_LIThe conserved expression pattern is governed by lineage-specific CREs. C_LIO_LIThose CREs harbor similar types of TFBSs such as Fox-family TFs. C_LI Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=94 SRC="FIGDIR/small/731870v1_ufig1.gif" ALT="Figure 1"> View larger version (22K): org.highwire.dtl.DTLVardef@c8c84dorg.highwire.dtl.DTLVardef@1d65668org.highwire.dtl.DTLVardef@c2d732org.highwire.dtl.DTLVardef@1be54a2_HPS_FORMAT_FIGEXP M_FIG C_FIG

Developmental Biology↗

bioRxiv2026

A Stronger Association Between Screen Time and Externalizing Problems in Typically Developing Children than in Children with Autism Spectrum Disorder

Excessive screen use is associated with childhood behavioral problems, but whether associations differ between typically developing (TD) children and those with autism spectrum disorder (ASD) is unclear. Our cross-sectional study included 108 children aged 5-9 years (61 TD, 47 ASD). ASD was diagnosed using standardized clinical instruments. Measures included parent-reported screen time (excluding TV/DVD), cognitive ability (K-ABC), and behavioral problems (Vineland-II). Screen time and externalizing problems were associated in the TD group (Spearmans {rho} = 0.361, p < 0.01), but not in the ASD group. In the regression model, screen time ({beta} = 0.40, t = 2.60, p < 0.05), ASD status ({beta} = 0.70, t = 8.30, p < 0.001), and their interaction ({beta} = -0.34, t = -2.06, p < 0.05) significantly predicted externalizing problems. Considering the diversity within the autism spectrum, future studies with larger sample sizes should consider individual heterogeneity when examining the association between behavioral outcomes and screen time.

scientific communication and education↗

bioRxiv2026

AtPUP5 functions as a plasma membrane flavin transporter regulating localized riboflavin distribution in Arabidopsis

Riboflavin (vitamin B{square}; RF) and its derivatives flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD) are indispensable cofactors for redox reactions in plants. While higher plants possess a conserved pathway for de novo riboflavin biosynthesis, how flavins are transported and spatially distributed between tissues remains unresolved. In particular, the molecular identity of plasma membrane transporters involved in flavin transport in plants remains largely unknown. Here, we identify Arabidopsis purine permease 5 (AtPUP5) as a plasma membrane-localized protein associated with riboflavin transport and its distribution in plants. Using a riboflavin-auxotrophic yeast mutant, we show that AtPUP5 enhances intracellular accumulation of RF and, to a lesser extent, FMN, whereas FAD accumulation is inefficient under the conditions tested. In planta, AtPUP5 overexpression increases RF accumulation following external application. In contrast, loss-of-function mutants do not display defects in bulk RF uptake at the whole-plant level, indicating that AtPUP5 is not essential for global riboflavin acquisition. Notably, AtPUP5 deficiency results in RF overaccumulation in reproductive organs, including inflorescences, siliques, and seeds, irrespective of external RF supply. This organ-specific phenotype is fully suppressed by genetic complementation and coincides spatially with strong AtPUP5 promoter activity in reproductive tissues. These findings suggest that AtPUP5 contributes to the regulation of localized riboflavin distribution in reproductive tissues. Together, our study provides a molecular framework for plasma membrane-mediated regulation of riboflavin distribution in plants and highlights spatial regulation as an important component of flavin homeostasis.

plant biology↗

bioRxiv2025

Altered Motor Gamma Activity and Hemispheric Lateralisation Reflect Perinatal Maturity in Preterm Children during Motor Control

Preterm birth, defined as delivery before 37 weeks of gestation, is associated with differences in neurodevelopment and an increased likelihood of motor challenges that may persist throughout childhood. However, the neurophysiological correlates of these motor differences remain insufficiently understood. Oscillatory activity in the primary motor cortex is closely linked to motor execution, yet motor-related oscillations have rarely been examined in children born preterm. In this cross-sectional observational study, we investigated motor-related gamma oscillations in 5- to 7-year-old children using a child-customised magnetoencephalography system. Nineteen children born full-term and 18 children born preterm of comparable age performed a child-friendly dominant-hand finger movement task. Movement-related gamma activity was quantified from bilateral precentral gyrus regions used as anatomical proxies for the primary motor cortices. The preterm group showed longer mean response times and greater intra-individual response-time variability than the full-term group (P = 0.003 and P = 0.030, respectively). Contralateral gamma power was also lower in the preterm group (full-term: 59.89 {+/-} 28.87%; preterm: 37.97 {+/-} 25.82%; t(35) = 2.43, P = 0.020, Cohen's d = 0.80). A significant Group x Hemisphere interaction (F(1, 35) = 13.36, P < 0.001, partial 2 = 0.276) further indicated differences in the hemispheric organisation of gamma activity between groups. The gamma laterality index was also lower in children born preterm (full-term: 0.24 {+/-} 0.21; preterm: -0.11 {+/-} 0.37; t(26.4) = 3.51, P = 0.002, Cohen's d = 1.17), consistent with reduced contralateral dominance. Across the whole sample, greater contralateral gamma lateralisation was associated with higher scores on the Hand Movements subtest of the Kaufman Assessment Battery for Children ({rho} = 0.40, P = 0.014, false discovery rate-adjusted q = 0.042) and earlier independent walking ({rho} = 0.57, P < 0.001, q = 0.002). The association with independent walking was also observed within the preterm group ({rho} = 0.78, P < 0.001, q = 0.002). These findings suggest that reduced contralateral gamma power and reduced hemispheric lateralisation in children born preterm may reflect differences in the developmental organisation of motor cortical networks. This study provides new insight into motor cortical organisation and its relationship with motor development following preterm birth.

neuroscience↗

bioRxiv2025

Retinoic acid-responsive hox genes in hoxba and hoxbb clusters direct pharyngeal pouch formation in zebrafish

The segmented pharyngeal apparatus is crucial for organ development specific to vertebrates, and its formation relies on the proper development of pharyngeal pouches. While retinoic acid (RA) is known to influence pouch formation, the downstream genes involved have been unclear. In this study, we demonstrate that zebrafish mutants lacking both the hoxba and hoxbb clusters--teleost-specific duplicates of the ancestral HoxB cluster--exhibit a significant loss of posterior pharyngeal pouches and related skeletal elements. This phenotype resembles that observed in raldh2 and pax1a;pax1b mutants. We identify hoxb1a and hoxb1b as RA-dependent genes expressed in the pharyngeal region that are essential for pouch formation. Morpholino-mediated knockdown of these genes replicated the pouch defects and decreased pax1a expression, indicating a regulatory pathway linking RA, Hox, and pax1. Our findings uncover a previously unrecognized role of Hox genes in early pouch segmentation and suggest that RA-responsive HoxB clusters were co-opted during vertebrate evolution to initiate pharyngeal regionalization.

developmental biology↗

bioRxiv2025

Genetic evidence: zebrafish hoxba and hoxbb clusters are essential for the anterior-posterior positioning of pectoral fins

Vertebrate paired appendages, such as the pectoral fins in fish and the forelimbs in tetrapods, arise at specific regions along the anterior-posterior axis of the body. Hox genes have long been considered prime candidates for determining the anteroposterior positioning of these paired appendages during development. Evidence from various model organisms, including mouse and chick, supports a role for Hox genes in limb positioning. However, despite extensive phenotypic analyses of numerous single and compound Hox knockout mice, clear genetic evidence for substantial defects in limb positioning has been limited, leaving questions unresolved. In a previous study, we generated seven distinct hox cluster-deficient mutants in zebrafish. Here, we provide genetic evidence that zebrafish hoxba;hoxbb cluster-deleted mutants specifically exhibit a complete lack of pectoral fins, accompanied by the absence of tbx5a expression in pectoral fin buds. In these mutants, tbx5a expression in the pectoral fin field of the lateral plate mesoderm fails to be induced at an early stage, suggesting a loss of pectoral fin precursor cells. Furthermore, the competence to respond to retinoic acid is lost in hoxba;hoxbb cluster mutants, indicating that tbx5a expression cannot be induced in the pectoral fin buds. We further identify hoxb4a, hoxb5a, and hoxb5b as pivotal genes underlying this process. Although the frameshift mutations in these hox genes do not recapitulate the absence of pectoral fins, we demonstrate that deletion mutants at these genomic loci show the absence of pectoral fins with low penetrance. Our results suggest that, by establishing the expression domains along the anteroposterior axis, hoxb4a, hoxb5a, and hoxb5b within hoxba and hoxbb clusters cooperatively determine the positioning of zebrafish pectoral fins through the induction of tbx5a expression in the restricted pectoral fin field. Our findings also provide insights into the evolutionary origin of paired appendages in vertebrates.

developmental biology↗

bioRxiv2025

Temperature vaulting: A method for screening selective, slow- and tight-binding inhibitors targeting kinases in their non-native state

A polypeptide folds into its protein tertiary structure in the native state through a folding intermediate in the non-native state. The transition between these states is thermodynamically driven. A folding intermediate of dual-specificity tyrosine phosphorylation-regulated kinase 1A (DYRK1A) autophosphorylates intramolecularly, whereas DYRK1A in the native state no longer catalyzes this reaction. The alteration in substrate specificity suggests a conformational transition of DYRK1A during its folding process. Consistent with this hypothesis, we identified FINDY (1), which inhibits the intramolecular autophosphorylation but not the intermolecular phosphorylation, suggesting that the folding intermediate possesses an alternative inhibitor-binding site. Meanwhile, it remains an issue that the methods for approaching the alternative binding site require an intricate assay tailored to the individual target. Here we show a method, designated as "temperature vaulting," for screening the non-native-state-targeted inhibitors of DYRK1A. Transient heating of recombinant DYRK1A protein drove the reversible transition between the native state and the non-native state targeted by FINDY (1). At physiological temperature, FINDY (1) slowly bound to the DYRK1A protein. These results indicate that transient heating accelerates the slow-binding process by assisting the protein to overcome the high-energy barrier leading to the target non-native state. The energy barrier also slowed down the dissociation process, resulting in tight binding between DYRK1A and FINDY (1). Furthermore, this study suggests that the dissociation rate underlies the inhibition selectivity of FINDY (1) between DYRK1A and its family kinase DYRK1B. This method enables the identification of slow- and tight-binding inhibitors that have been missed in conventional assays. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=112 SRC="FIGDIR/small/632643v1_ufig1.gif" ALT="Figure 1"> View larger version (26K): org.highwire.dtl.DTLVardef@be5661org.highwire.dtl.DTLVardef@1925beorg.highwire.dtl.DTLVardef@fceb5borg.highwire.dtl.DTLVardef@bfbf91_HPS_FORMAT_FIGEXP M_FIG C_FIG HIGHLIGHTSA temperature vaulting method facilitated the screening of a slow- and tight-binding inhibitor targeting DYRK1A in the non-native state. A structure-activity relationship study of FINDY (1) demonstrated that a slight alteration in chemical structure impacts the inhibition kinetics. A molecular dynamics simulation of DYRK1A revealed binding-ready conformations for FINDY (1). The dissociation rate may underlie the inhibition selectivity of FINDY (1) between DYRK1A and DYRK1B in cellular systems.

biophysics↗

bioRxiv2024

Selective agonism of GPR34 stimulates microglial uptake and clearance of amyloid β fibrils

Microglia, the primary immune cells of the central nervous system, play a crucial role in maintaining brain homeostasis through phagocytosis of various substrates, including amyloid-{beta} (A{beta}) fibrils, a hallmark of Alzheimer disease (AD) pathology. However, the molecular mechanisms regulating microglial A{beta} uptake remain poorly understood. Here, we identified GPR34, a Gi/o-coupled receptor highly expressed in microglia, as a novel regulator of fibrillar A{beta} phagocytosis. Treatment with a selective GPR34 agonist, M1, specifically enhanced uptake of A{beta} fibrils, but not its monomer or oligomer, in both mouse and human microglia. Mechanistically, M1 reduced intracellular cAMP levels, which inversely correlated with A{beta} uptake activity. Importantly, a single intrahippocampal injection of M1 in an AD mouse model significantly increased microglial A{beta} uptake in vivo. Furthermore, single-nucleus RNA-sequencing analysis of Japanese AD patient samples revealed a significant reduction of GPR34 expression in microglia from AD patients compared to controls. We also observed an age-dependent decline in microglial GPR34 expression in both human and mouse datasets, suggesting a potential contribution of GPR34 downregulation to age-related A{beta} accumulation and AD risk. Collectively, our findings identify GPR34 as a promising target for modulating microglial A{beta} clearance and highlight the therapeutic potential of GPR34 agonists in AD. Significance statementAlzheimer disease (AD) is characterized by amyloid-{beta} (A{beta}) accumulation in the brain. Microglia, the brains immune cells, play a crucial role in the metabolism of A{beta}. We discovered that activating the microglial receptor GPR34 with a selective agonist enhances the phagocytosis of A{beta} fibrils, a key pathogenic form of A{beta}. Importantly, GPR34 expression decreases with aging and AD progression, potentially contributing to impaired A{beta} clearance. Our findings highlight GPR34 as a promising therapeutic target for AD, as boosting its activity could promote A{beta} clearance and slow disease progression. This study provides valuable insights into microglial function in AD and offers a novel strategy for developing disease-modifying therapies.

neuroscience↗

bioRxiv2023

Sexually dimorphic dynamics of the microtubule network in medaka (Oryzias latipes) germ cells

Oogenesis is the process through which ovarian germ cells enter meiosis and acquire essential characteristics of an egg, such as an increase in follicular size and deposition of maternal factors. In vertebrates, however, the pathways that initiate oogenic processes after germ cell sex determination remain elusive. Here we report a dome-shaped microtubule structure that is maintained during oogenesis. This structure is established in primordial germ cells and maintained in gonocytes and stem-type germ cells in a foxl3-independent manner. dmrt1 is required for disruption of the dome structure in differentiating spermatogonia. In addition, the dome structure accumulates mitochondria and Golgi apparatus, and is replaced by the Balbiani body, an oocyte-specific aggregate producing animal-vegetal polarity, suggesting a role for this structure in organelle transfer and oocyte polarization. Our findings show the presence of a pathway regulating a sexually dimorphic microtubule network independent of germ cell feminization by foxl3. Summary StatementA dome-shaped microtubule structure leading to oocyte polarity was identified in germ cells. Genetic pathways involved in the formation and destabilization of the structure during germ cell sex determination were clarified.

developmental biology↗

bioRxiv2023

Epigenetic mechanisms to propagate histone acetylation by p300/CBP

Histone acetylation is important for the activation of gene transcription but little is known about its direct read/write mechanisms. Here, we report cryo-electron microscopy structures in which a p300/CBP multidomain monomer recognizes histone H4 N-terminal tail (NT) acetylation (ac) in a nucleosome and acetylates non-H4 histone NTs within the same nucleosome. p300/CBP not only recognized H4NTac via the bromodomain pocket responsible for reading, but also interacted with the DNA minor grooves via the outside of that pocket. This directed the catalytic center of p300/CBP to one of the non-H4 histone NTs. The primary target that p300 writes by reading H4NTac was H2BNT, and H2BNTac promoted H2A-H2B dissociation from the nucleosome. We propose a model in which p300/CBP replicates histone NT acetylation within the H3-H4 tetramer to inherit epigenetic storage, and transcribes it from the H3-H4 tetramer to the H2B-H2A dimers to activate context-dependent gene transcription through local nucleosome destabilization.

biochemistry↗

bioRxiv2022

Proton-pumping rhodopsins in marine diatoms

Diatoms are a major phytoplankton group responsible for about 20% of Earths primary production. They carry out photosynthesis inside the plastid, an organelle obtained through eukaryote-eukaryote endosymbiosis. Recently, microbial rhodopsin, a photoreceptor distinct from chlorophyll-based photosystems, has been identified in certain diatoms. However, the physiological function of diatom rhodopsin is not well understood. Here we show that the diatom rhodopsin acts as a light-driven proton pump and localizes to the outermost membrane of the four membrane-bound complex plastids. Heterologous expression techniques were used to investigate the protein function and subcellular localization of diatom rhodopsin. Using model simulations, we further evaluated the physiological role of the acidic pool in the plastid produced by proton-transporting rhodopsin. Our results propose that the rhodopsin-derived acidic pool may be involved in a photosynthetic CO2-concentrating mechanism and assist CO2 fixation in diatom cells.

microbiology↗

bioRxiv2021

Detection of the 40-Hz Auditory Steady-state Response with Optically Pumped Magnetometers

Magnetoencephalography (MEG) is a functional neuroimaging technique that noninvasively detects the brain magnetic field from neuronal activations. Conventional MEG measures brain signals using superconducting quantum interference devices (SQUIDs). SQUID-MEG requires a cryogenic environment involving a bulky non-magnetic dewar and the consumption of liquid helium, which restricts the variability of the sensor array and the gap between the cortical sources and sensors. Recently, miniature optically pumped magnetometers (OPMs) have been developed and commercialized. OPMs do not require cryogenic cooling and can be placed within millimeters from the scalp. In the present study, we arranged six OPM sensors on the temporal area to detect auditory-related brain responses in a two-layer magnetically shielded room. We presented the auditory stimuli of 1-kHz pure-tone bursts with 200-ms duration and obtained the M50 and M100 components of auditory evoked fields. We delivered the periodic stimuli with a 40-Hz repetition rate and observed the gamma-band power changes and inter-trial phase coherence of auditory steady-state responses at 40 Hz. We found that the OPM sensors have a performance comparable to that of conventional SQUID-MEG sensors, and our results suggest the feasibility of using OPM sensors for functional neuroimaging and brain-computer interface applications.

neuroscience↗

bioRxiv2020

Kcns3 Deficiency Disrupts Parvalbumin Neuron Physiology in Mouse Prefrontal Cortex: Implications for the pathophysiology of schizophrenia

The unique fast spiking (FS) phenotype of cortical parvalbumin-positive (PV) neurons depends on multiple subtypes of voltage-gated potassium channels (Kv). PV neurons selectively express Kcns3, the gene encoding Kv9.3 subunits, suggesting that Kcns3 expression is critical for the FS phenotype. KCNS3 expression is lower in PV neurons in schizophrenia, but the effects of this alteration are unclear, because Kv9.3 subunit function is poorly understood. We therefore assessed the role of Kv9.3 subunits in PV neuron function by combining gene expression analyses, computational modeling, and electrophysiology in acute slices from the cortex of Kcns3-deficient mice Kcns3 mRNA levels were ~50% lower in cortical PV neurons from Kcns3-deficient relative to wildtype mice. While silent per se, Kv9.3 subunits are believed to amplify the Kv2.1 current in Kv2.1-Kv9.3 channel complexes. Hence, to assess the consequences of reducing Kv9.3 levels, we simulated the effects of decreasing the Kv2.1-mediated current in a computational model. The FS cell model with reduced Kv2.1 produced spike trains with irregular inter-spike intervals, or stuttering, and greater Na+ channel inactivation, possibly due to a smaller afterhyperpolarization. As in the computational model, PV basket cells (PVBCs) from Kcns3-deficient mice displayed spike trains with strong stuttering, which depressed PVBC firing, and smaller afterhyperpolarization. Moreover, Kcns3 deficiency impaired the recruitment of PVBCs by stimuli mimicking synaptic input during cortical UP states, which elicited bursts of spikes at gamma frequency. Our data suggest that Kv9.3 subunits are critical for PVBC physiology, and that KCNS3 deficiency in schizophrenia may impair the substrate of gamma oscillations. Significance statementIn the neocortex, Kcns3, the gene encoding voltage-dependent potassium (Kv) channel subunits Kv9.3, is selectively expressed by parvalbumin-positive (PV) neurons. Moreover, KCNS3 expression is decreased in PV neurons in schizophrenia. Kv 9.3 subunits are believed to amplify the current mediated by Kv2.1 subunits, however Kv9.3 function has not been investigated in PV cells. Here, simulations in a computational model and electrophysiological experiments with Kcns3-deficient mice revealed that Kcns3 deficiency disrupts repetitive firing in cortical PV neurons, possibly enhancing Na+ channel inactivation, and particularly with stimuli eliciting firing at gamma frequency band (30-80Hz). Our results suggest that Kv9.3 subunits are essential for PV neuron electrophysiology and that KCNS3 deficiency likely contributes to PV neuron dysfunction and gamma oscillation impairments in schizophrenia.

neuroscience↗

bioRxiv2020

Artificial intelligence based computational framework for drug-target prioritization and inference of novel repositionable drugs for Alzheimer's disease

BackgroundIdentification of novel therapeutic targets is a key for successful drug development. However, the cost to experimentally identify therapeutic targets is huge and only 400 genes are targets for FDA-approved drugs. Therefore, it is inevitable to develop powerful computational tools to identify potential novel therapeutic targets. Because proteins make their functions together with their interacting partners, a protein-protein interaction network (PIN) in human could be a useful resource to build computational tools to investigate potential targets for therapeutic drugs. Network embedding methods, especially deep-learning based methods would be useful tools to extract an informative low-dimensional latent space that contains enough information required to fully represent original high-dimensional non-linear data of PINs. ResultsIn this study, we developed a deep learning based computational framework that extracts low-dimensional latent space embedded in high-dimensional data of the human PIN and uses the features in the latent space (latent features) to infer potential novel targets for therapeutic drugs. We examined the relationships between the latent features and the representative network metrics and found that the network metrics can explain a large number of the latent features, while several latent features do not correlate with all the network metrics. The results indicate that the features are likely to capture information that the representative network metrics can not capture, while the latent features also can capture information obtained from the network metrics. Our computational framework uses the latent features together with state-of-the-art machine learning techniques to infer potential drug target genes. We applied our computational framework to prioritized novel putative target genes for Alzheimers disease and successfully identified key genes for potential novel therapeutic targets (e.g., DLG4, EGFR, RAC1, SYK, PTK2B, SOCS1). Furthermore, based on these putative targets, we inferred repositionable candidate-compounds for the disease (e.g., Tamoxifen, Bosutinib, and Dasatinib) DiscussionsOur computational framework could be powerful computational tools to efficiently prioritize new therapeutic targets and drug repositioning. It is pertinent to note here that our computational platform is easily applicable to investigate novel potential targets and repositionable compounds for any diseases, especially for rare diseases.

bioinformatics↗

bioRxiv2020

Rational design and implementation of a chemically inducible hetero-trimerization system

Chemically inducible dimerization (CID) uses a small molecule to induce binding of two different proteins. CID tools exemplified by the FKBP/FRB/rapamycin system have been widely employed to probe molecular events inside and outside cells. While various CID tools are available, chemically inducible trimerization (CIT) has not been developed, due to inherent challenges in designing or identifying a chemical that simultaneously binds three proteins with high affinity and target specificity. Nevertheless, by introducing a third recruitable component, CIT could enable versatile applications. Here, we devised the CIT by rationally splitting FRB and FKBP. Based on cellular and structural datasets, select split pairs of FRB or FKBP underwent efficient trimerization with full length FKBP or FRB, respectively, upon addition of rapamycin. We also demonstrated its potential for cellular applications by rapidly inducing tri-organellar plasma membrane-ER-mitochondria junctions, and by perturbing intended membrane lipids exclusively at the plasma membrane-ER membrane contact sites. By conferring one additional condition to what is achievable with CID, CIT expands the types of manipulation in single live cells, to address cell biology questions otherwise intractable, and engineer cell functions for future synthetic biology applications.

cell biology↗

bioRxiv2019

Disruption of a RAC1-centred protein interaction network is associated with Alzheimer’s disease pathology and causes age-dependent neurodegeneration

The molecular biological mechanisms of Alzheimers disease (AD) involve disease-associated cross-talk through many genes and include a loss of normal as well as a gain of abnormal interactions among genes. A protein domain network (PDN) is a collection of physical bindings that occur between protein domains, and the states of the PDNs in patients with AD are likely to be perturbed compared to those in normal healthy individuals. To identify PDN changes that cause neurodegeneration, we analysed the PDNs that occur among genes co-expressed in each of three brain regions at each stage of AD. Our analysis revealed that the PDNs collapsed with the progression of AD stage and identified five hub genes, including Rac1, as key players in PDN collapse. Using publicly available gene expression data, we confirmed that the mRNA expression level of the RAC1 gene was downregulated in the entorhinal cortex (EC) of AD brains. To test the causality of these changes in neurodegeneration, we utilized Drosophila as a genetic model and found that modest knockdown of Rac1 in neurons was sufficient to cause age-dependent behavioural deficits and neurodegeneration. Finally, we identified a microRNA, hsa-miR-101-3p, as a potential regulator of RAC1 in AD brains. As the Braak neurofibrillary tangle (NFT) stage progressed, the expression levels of hsa-miR-101-3p were upregulated specifically in the EC. Furthermore, overexpression of hsa-miR-101-3p in the human neuronal cell line SH-SY5Y caused RAC1 downregulation. These results highlight the utility of our integrated network approach for identifying causal changes leading to neurodegeneration in AD.

genomics↗

bioRxiv2018

Enhancer variants associated with Alzheimer’s disease affect gene expression via chromatin looping

BackgroundGenome-wide association studies (GWASs) have identified single-nucleotide polymorphisms (SNPs) that may be genetic factors underlying Alzheimers disease (AD). However, how these AD-associated SNPs (AD SNPs) contribute to the pathogenesis of this disease is poorly understood because most of them are located in non-coding regions, such as introns and intergenic regions. Previous studies reported that some disease-associated SNPs affect regulatory elements including enhancers. We hypothesized that non-coding AD SNPs are located in enhancers and affect gene expression levels via chromatin loops.\n\nResultsWe examined enhancer locations that were predicted in 127 human tissues or cell types, including ten brain tissues, and identified chromatin-chromatin interactions by Hi-C experiments. We report the following findings: (1) nearly 30% of non-coding AD SNPs are located in enhancers; (2) expression quantitative trait locus (eQTL) genes affected by non-coding AD SNPs within enhancers are associated with amyloid beta clearance, synaptic transmission, and immune responses; (3) 95% of the AD SNPs located in enhancers co-localize with their eQTL genes in topologically associating domains suggesting that regulation may occur through chromatin higher-order structures; (4) rs1476679 spatially contacts the promoters of eQTL genes via CTCF-CTCF interactions; (5) the effect of other AD SNPs such as rs7364180 is likely to be, at least in part, indirect through regulation of transcription factors that in turn regulate AD associated genes.\n\nConclusionOur results suggest that non-coding AD SNPs may affect the function of enhancers thereby influencing the expression levels of surrounding or distant genes via chromatin loops. This result may explain how some non-coding AD SNPs contribute to AD pathogenesis.

genomics↗