Biology subjects

Takahashi, N.

Publications and source records attributed to Takahashi, N..

At least 37 records · Page 2Linked to original sources

bioRxiv2024

Bioinformatic evaluation of the potential oral-gut translocation of periodontal pathogens in patients with colorectal polyps

ObjectiveThis study aimed to characterize the profiles of the oral and gut microbiota of patients with colorectal polyps using 16S rRNA gene sequencing and bioinformatic approaches. BackgroundPrevious studies have shown microbial translocation from the oral cavity to the gut, implying pathogenic impacts on gastroesophageal disease, including colorectal cancer (CRC). However, its details remain unclear. MethodsTwenty patients scheduled for endoscopic colorectal polypectomy were enrolled in this study. Oral samples (saliva and subgingival dental plaque) and intestinal samples (feces and swab of intestinal mucosa) were collected during preoperative and 6-month-postoperative reassessment periods. After sequencing the V3-V4 region of the bacterial 16S rRNA gene, several bioinformatic analyses (bacterial composition, diversity, core microbiome, and shared ASV) were performed on pre- and postoperative samples for each subject. ResultsThe bacterial composition was dominated by Bacteroides, Streptococcus, Fusobacterium, Veillonella, and Prevotella_7 in all four samples. Beta diversity analysis using weighted UniFrac distance distinctly segregated the samples between oral and intestinal environments in the principal coordinate analysis plot. Core microbiome analysis revealed that Streptococcus and Porphyromonas were dominantly shared in intra-oral environments. Additionally, alongside Streptococcus, periodontitis-related bacteria, such as Veillonella, Fusobacterium, Porphyromonas, Prevotella_7, Haemophilus, and Prevotella, were identified as shared genera between oral and intestinal environments. Finally, shared ASV analysis demonstrated that Streptococcus was shared in the oral and intestinal environments of most patients, while periodontal pathogens were shared in some patients. ConclusionsThe core microbiome and shared ASV analyses revealed that several genes are shared between oral and intestinal environments in patients with colorectal polyps, indicating the oral-gut translocation of periodontitis-related bacteria. Further large-scale studies are needed to elucidate their involvement in CRC.

bioinformatics↗

bioRxiv2024

CD34-positive monocytes are highly susceptible to HIV-1

HIV-1 persists in cellular reservoirs despite effective combined antiretroviral therapy (cART). CD4+ T cells are a well-known reservoir, but there is evidence suggesting that myeloid cells, including circulating monocytes, are also a clinically relevant reservoir. However, it is not fully understood which subsets of monocytes are preferentially infected in vivo. Here, we show that a monocyte fraction expressing a stem cell marker CD34 is more susceptible to HIV-1 infection than the CD34-negative major subset. In cART-untreated viremic individuals, the CD34+ fraction increased in the percentage in total monocytes, and harbored higher copies of proviral DNA than the major subset. Consistent with this, the CD34+ fraction expressed HIV-1 receptors CD4 and CCR5 at higher levels and HIV-1 restriction factors MX2 and SAMHD1 at lower levels. Interestingly, proviral DNA was still detectable in the CD34+ fraction of cART-treated virologically suppressed individuals. CD34+ monocytes were also present in lymph nodes, and expressed CD4 and CCR5 at higher levels than the major subset, as observed in peripheral blood. Moreover, CD34+ monocytes present in peripheral blood and lymph nodes highly expressed CCR7 and sphingosine-1-phosphate receptor 1 (S1PR1), critical regulators of in vivo cellular trafficking. Collectively, our findings raise the new possibility that lymph node CD34+ monocytes, which originate from the circulation, are infected with HIV-1 owing to their high susceptibility to HIV-1, and return to circulation, which explains the detection of proviral DNA in peripheral CD34+ monocytes even after long-term cART.

immunology↗

bioRxiv2024

Microenvironment Shapes Cell State, Plasticity, and Heterogeneity of Small Cell Lung Cancer

Small-cell lung cancer (SCLC) is the most fatal form of lung cancer. Intra-tumoral heterogeneity, marked by neuroendocrine (NE) and non-neuroendocrine (non-NE) cell states, defines SCLC, but the drivers of SCLC plasticity are poorly understood. To map the landscape of SCLC tumor microenvironment (TME), we apply spatially resolved transcriptomics and quantitative mass spectrometry-based proteomics to metastatic SCLC tumors obtained via rapid autopsy. The phenotype and overall composition of non-malignant cells in the tumor microenvironment (TME) exhibits substantial variability, closely mirroring the tumor phenotype, suggesting TME-driven reprogramming of NE cell states. We identify cancer-associated fibroblasts (CAF) as a crucial element of SCLC TME heterogeneity, contributing to immune exclusion, and predicting exceptionally poor prognosis. Together, our work provides a comprehensive map of SCLC tumor and TME ecosystems, emphasizing their pivotal role in SCLCs adaptable nature, opening possibilities for re-programming the intercellular communications that shape SCLC tumor states.

cancer biology↗

bioRxiv2023

Early-stage neural processing reveals distinctive responses to saliency-differentiated colors in various types of color vision

Individuals with minority color vision phenotypes have been reported to exhibit enhanced color discrimination and color recognition, which deviate from predictions based on their receptoral sensitivities. However, the specific mechanisms underlying this enhanced sensitivity remain unclear. In this study, we examined the commonality and diversity of neural activity between typical and anomalous trichromats in response to differences in color saliency. Electroencephalography was recorded during an oddball task, in which participants discriminated each of two target stimuli, blue-green and red, from a green standard stimulus. The chromaticity of the stimulus was identical across participants, whereas the relationship of saliency between the target stimuli was expected to be reversed between color vision types. The spatiotemporal dynamics of event-related potentials (ERPs) were analyzed using cluster-based permutation tests. Typical trichromats demonstrated faster behavioral and neural responses to the more salient red target stimulus, with pronounced neural activity spreading from the occipital to the parietal regions in the comparison between the target stimuli. Anomalous trichromats also exhibited similar temporal patterns toward the more salient target stimulus when each target stimulus was compared with the green standard stimulus, indicating comparable processing toward saliency across color vision types. Although a similarity was observed, neither behavioral nor neural responses in anomalous trichromats reflected saliency contrast differences. In addition, a comparative analysis of ERPs between color vision types did not reveal any distinct differences in either target stimulus. Given the large variations in color sensitivity in individuals with anomalous trichromacy, further investigation is required to understand the detailed neural processing in individuals with various color vision types.

neuroscience↗

bioRxiv2023

ZFP57 is a regulator of postnatal growth and life-long health

Early-life factors, including nutrition, shape long-term health outcomes. Despite the essential role of lactation in maternal nutritional support, the influence of epigenetic factors on lactation and postnatal growth remains poorly understood. Zinc-finger protein 57 (ZFP57), is an epigenetic regulator of genomic imprinting, a process that directs gene expression based on parental origin, playing a vital role in mammalian prenatal growth. Here, we identify a novel function of ZFP57 in regulating the mammary gland, where it serves as a key modulator of postnatal resource control, independently of imprinted genes. ZFP57 influences multiple aspects of mammary gland function, including ductal branching and cellular homeostasis. Its absence leads to significant differential gene expression, related to alveologenesis, lactogenesis and milk synthesis, associated with delayed lactation and altered milk composition. This results in life-long impacts on offspring including the development of metabolic syndrome. Cross-fostering reveals intricate dynamics between mother and offspring during lactation. Pups raised by a dam of a different genotype than their birth mother exhibit exacerbated metabolic features in adulthood, providing additional insight into the programming of offspring long-term health by maternal context. This study deepens our understanding of the interplay between epigenetic factors, lactation, and postnatal resource control and identifies ZFP57 as a major regulator of both pre and postnatal resource control in mammals.

developmental biology↗

bioRxiv2023

ULK1-regulated AMP sensing by AMPK and its application for the treatment of chronic kidney disease

AMP-activated protein kinase (AMPK) is a central kinase involved in energy homeostasis. Increased intracellular adenosine monophosphate (AMP) levels result in AMPK activation through the binding of AMP to the {gamma}-subunit of AMPK. Recently, we reported that AMP-induced AMPK activation is impaired in the kidneys in chronic kidney disease (CKD) despite an increase in the AMP/ATP ratio. However, the mechanisms by which AMP sensing is disrupted in CKD are unclear. In this study, we identified mechanisms of energy homeostasis in which Unc-51-like kinase 1 (ULK1)-dependent phosphorylation of AMPK{gamma}1 at Ser260/Thr262 promotes AMP sensitivity of AMPK. AMPK activation by AMP was impaired in Ulk1-/- mice despite an increased AMP/ATP ratio. We also demonstrated that MK8722, an allosteric AMPK activator, activates AMPK in the kidneys of a CKD mouse model via a pathway that is independent of AMP sensing. MK8722 treatment significantly attenuates the deterioration of renal function in CKD and is a potential therapeutic option in CKD therapeutics.

molecular biology↗

bioRxiv2023

Local changes in potassium ions modulate dendritic integration

During neuronal activity the extracellular concentration of potassium ions ([K+]o) increases substantially above resting levels, but it remains unclear what role these [K+]o changes play in dendritic integration of synaptic inputs. We used mathematical formulations and biophysical modeling to explore the role of activity-dependent K+ changes near dendritic segments of a visual cortex pyramidal neuron, receiving synaptic inputs tuned to stimulus orientation. We found that the fine-scale spatial arrangement of inputs dictates the magnitude of [K+]o changes around the dendrites: Dendritic segments with similarly-tuned inputs can attain substantially higher [K+]o increases than segments with diversely-tuned inputs. These [K+]o elevations in turn increase dendritic excitability, leading to more robust and prolonged dendritic spikes. Ultimately, these local effects amplify the gain of neuronal input-output transformations, causing higher orientation-tuned somatic firing rates without compromising orientation selectivity. Our results suggest that local activity-dependent [K+]o changes around dendrites may act as a "volume knob" that determines the impact of synaptic inputs on feature-tuned neuronal firing.

neuroscience↗

bioRxiv2023

Type 1 immunity enables neonatal thymic ILC1 production

Thymic atrophy occurs following type 1 inflammatory conditions like viral infection and sepsis, resulting in cell death and disruption of T-cell development. However, it remains undetermined whether the thymus actively contributes to the immune response. Thus, we cultured neonatal thymus ex vivo with the type 1 cytokines IL-12 plus IL-18, resulting in a rapid shift from steady-state T-cell development to the production, expansion, and thymic exit of CXCR6+CD62L- type 1 innate lymphoid cells (ILC1s). Single-cell RNA-sequencing and functional assays identified these cells as embryonic-wave-derived KLRG1+ ILC1s that mainly differentiated from immature neonatal thymic ILC1s. Confocal 3D imaging confirmed neonatal thymic ILC1 expansion during MCMV infection. Furthermore, thymic grafts revealed in vivo thymic ILC1 egress and type 1 inflammation-induced homing of thymus-derived KLRG1+ ILC1s to the liver and peritoneal cavity. Altogether, our data reveal a novel thymic function where type 1 immunity enables the production and peripheral homing of thymic-derived ILC1s. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=185 SRC="FIGDIR/small/530451v1_ufig1.gif" ALT="Figure 1"> View larger version (56K): org.highwire.dtl.DTLVardef@d768corg.highwire.dtl.DTLVardef@1e20d77org.highwire.dtl.DTLVardef@1e206bforg.highwire.dtl.DTLVardef@292108_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

bioRxiv2023

Role of acetoacetyl-CoA synthetase in glucose uptake by HepG2 cells

Accelerated glucose metabolism is a common feature of cancer cells and represents a potential therapeutic target. Recent studies have revealed that lipid metabolism is related to glucose me-tabolism, especially glucose uptake. Acetoacetyl-CoA synthetase (AACS) converts acetoacetate, a ketone body, to acetoacetyl-CoA, which is incorporated into cholesterol and fatty acids. The AACS gene is highly expressed in HepG2 cells but not in the human normal liver. These results suggest a correlation between AACS and glucose metabolism. Therefore, we examined the relationship between AACS and glucose uptake in hepatocellular carcinoma (HepG2) cells. The expression of AACS was significantly upregulated when HepG2 cells were exposed to high concentrations of glucose. Lentiviruses, which code for shRNA against AACS (shAACS), were used to determine whether AACS knockdown affects the glucose uptake in HepG2 cells. AACS knockdown signifi-cantly reduced glucose uptake and increased the concentration of ketone bodies in the media, and treatment with {beta}-hydroxybutyrate, a ketone body, attenuated glucose uptake. Moreover, the knockdown of AACS, i.e., the increased concentration of the intracellular ketone body, slightly attenuated cell proliferation and significantly increased the sensitivity to the anticancer agent sorafenib. These results suggest that AACS plays an important role in glucose uptake and cell proliferation and that ketone bodies may compete with glucose as an important energy source for cancer cells.

molecular biology↗

bioRxiv2023

Mitotic heritability of DNA methylation at intermediately methylated sites is imprecise

DNA methylation is considered a stable epigenetic mark due to its presumed long-term inheritance through cell divisions. Here, we perform high-throughput bisulfite sequencing on clonally derived cell lines to quantitatively measure mitotic methylation inheritance at the nucleotide level. We find that although DNA methylation is generally faithfully maintained at hypo- and hypermethylated sites, this is not the case at intermediately methylated CpGs. Low fidelity intermediate methylation is interspersed throughout the genome and within genes with no or low transcriptional activity. Moreover, we determine that the probabilistic changes that occur at intermediately methylated sites are due to DNMT1 rather than DNMT3A/3B activity. The observed lack of clonal inheritance at intermediately methylated sites challenges the concept of DNA methylation as a consistently stable epigenetic mark.

genetics↗

bioRxiv2022

ATR inhibition augments the efficacy of lurbinectedin in small cell lung cancer

Abstract/SummarySmall cell lung cancer (SCLC) is the most lethal type of lung cancer. Specifically, MYC-driven non-neuroendocrine SCLC are particularly resistant to standard therapies. Lurbinectedin was recently approved for the treatment of relapsed SCLC, but combinatorial approaches are needed to increase the depth and duration of responses to lurbinectedin. Using high-throughput screens, we found inhibitors of ataxia telangiectasia-mutated and rad3-related (ATR) as the most effective agents for augmenting lurbinectedin efficacy. First-in-class ATR inhibitor berzosertib synergized with lurbinectedin in multiple SCLC cell lines, organoid and in-vivo models. Mechanistically, ATR inhibition abrogated S-phase arrest induced by lurbinectedin and forced cell-cycle progression causing mitotic catastrophe and cell death. High CDKN1A/p21 expression was associated with decreased synergy due to G1 arrest, while increased levels of ERCC5/XPG were predictive of increased combination efficacy. Importantly, MYC-driven non-neuroendocrine tumors which were resistant to first-line therapies displayed decreased CDKN1A/p21 expression and increased ERCC5/XPG indicating they were primed for response to lurbinectedin-berzosertib combination. The combination is being assessed in a clinical trial NCT04802174. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=198 SRC="FIGDIR/small/520783v1_ufig1.gif" ALT="Figure 1"> View larger version (63K): org.highwire.dtl.DTLVardef@19acf72org.highwire.dtl.DTLVardef@a9703forg.highwire.dtl.DTLVardef@86592org.highwire.dtl.DTLVardef@1448372_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2022

Local induction of IAA5 and IAA29 promotes DNA damage-triggered stem cell death in Arabidopsis roots

Plants generate organs continuously during post-embryonic development, thus how to preserve stem cells in changing environments is crucial for their survival. Genotoxic stress threatens genome stability in all somatic cells, whereas, in the meristem, only stem cells undergo cell death in response to DNA damage, followed by stem cell replenishment. It was previously shown that inhibition of downward auxin flow in roots participates in DNA damage-induced stem cell death; however, how cell death is confined to stem cells in tissues with reduced auxin content remains elusive. Here we show that, in response to DNA double-strand breaks, the Aux/IAA family members IAA5 and IAA29, which encode the negative regulators of auxin signaling, were locally induced in vascular stem cells and their daughters in Arabidopsis roots. This is an active response to DNA damage in which the transcription factor SUPPRESSOR OF GAMMA RESPONSE 1 directly induces their expression. In the iaa5 iaa29 double mutant, DNA damage-induced stem cell death was significantly suppressed, while it was fully restored by the expression of a stable form of IAA5 in vascular stem cells. Our genetic data revealed that both the suppression of auxin signaling and reduced auxin content are prerequisite for cell death induction, suggesting the central role in maintaining genome integrity in stem cells. One-sentence summaryThe induction of IAA5 and IAA29 promotes stem cell death in Arabidopsis roots under DNA stress.

plant biology↗

bioRxiv2022

Subtyping of Small Cell Lung Cancer using plasma cell-free nucleosomes

Emerging data on small cell lung cancer (SCLC), an aggressive malignancy with exceptionally poor prognosis, support subtypes driven by distinct transcription regulators, which engender unique therapeutic vulnerabilities. However, the translational potential of these observations is limited by access to tumor biopsies. Here, we leverage chromatin immunoprecipitation of cell-free nucleosomes carrying active chromatin modifications followed by sequencing (cfChIP-seq) on 442 plasma samples from individuals with advanced SCLC, neuroendocrine carcinomas (NEC), non-SCLC cancers, and healthy adults. Beyond providing reliable estimates of SCLC circulating free DNA tumor fraction, cfChIP-seq captures the unique epigenetic states of SCLC tissue- and cell-of-origin. Comparison of cfChIP-seq signals to matched tumor transcriptomes reveals genome-wide concordance, establishing a direct link between gene expression in the tumor and plasma cell-free nucleosomes. Exploiting this link, we develop a classifier that discriminates between SCLC lineage-defining transcription factor subtypes based on cfChIP-seq data. This work sets the stage to non-invasively profile SCLC transcriptomes using plasma cfDNA histone modifications.

cancer biology↗

bioRxiv2021

Computational analysis reveals similarities and differences between SCLC subtypes

Small cell lung cancer (SCLC) is a neuroendocrine malignancy with dismal survival rates. Previous studies have revealed inter and intra tumoral heterogeneity of SCLC driven by neuroendocrine differentiation and multiple gene expression signatures have been proposed to classify the distinct SCLC molecular subtypes However, few questions remain unanswered: a) how many SCLC subtypes exist? b) how similar or different are these subtypes?, c) which gene list(s) can be used to identify those specific subtypes? Here, we show that irrespective of the three gene sets (33 genes, 50 genes, 105 genes) proposed in different studies to classify SCLC into different subtypes, the markers of phenotypic heterogeneity in SCLC form a "teams" like pattern of co-expressed modules. Moreover, the 105 geneset could classify SCLC cell lines into five clusters, three of which can be distinctly mapped to the SCLC-A, SCLC-N and SCLC-Y subtypes. Intriguingly, we noticed a high degree of similarity in the transcriptional landscape of two non-neuroendocrine subtypes: SCLC-Y and SCLC-I*, as well as in their enrichment of EMT. Thus, our analysis elucidates the landscape of phenotypic heterogeneity enabling diverse SCLC subtypes.

cancer biology↗

bioRxiv2021

Subnuclear localisation is associated with gene activation not repression or parental origin at the imprinted Dlk1-Dio3 locus

At interphase, de-condensed chromosomes have a non-random three-dimensional architecture within the nucleus, however, little is known about the extent to which nuclear organisation might influence expression or vice versa. Here, using imprinting as a model, we use 3D RNA- and DNA-fluorescence-in-situ-hybridisation in normal and mutant mouse embryonic stem cells to assess the relationship between imprinting control, gene expression and allelic distance from the nuclear periphery. We compared the two parentally inherited imprinted domains at the Dlk1-Dio3 domain and find a small but reproducible trend for the maternally inherited domain to be further away from the periphery if the maternally expressed gene Gtl2/Meg3 is active compared to when it is silenced. Using Zfp57KO ES cells, which harbour a paternal to maternal epigenotype switch, we observe active alleles significantly further away from the nuclear periphery with the distance from the periphery being proportional to the number of alleles active within the cell. This distribution of alleles suggests an activating effect of the nuclear interior rather than a repressive association with the nuclear periphery. Although we see a trend for the paternally inherited copy of the locus to be closer to the nuclear periphery, this appears to be linked to stochastic gene expression differences rather than parental origin. Our results suggest that transcriptional activity, rather than transcriptional repression or parental origin, defines sub-nuclear localisation at an endogenous imprinted domain. Author summaryGenomic imprinting is an epigenetically regulated process that results in the preferential expression of a subset of developmentally regulated genes from maternally or paternally inherited chromosomes. We have used imprinted genes as a model system to investigate the relationship between the localisation of genes within the cell nucleus and their active expression while at the same time distinguishing gene repression by genomic imprinting, and gene repression by other mechanisms that act on the active allele. We find that there is a significant correlation between transcription and distance to the edge of the nucleus for the Gtl2/Meg3 gene in the imprinted Dlk1-Dio3 region. However, this correlation has a very small effect size and the nuclear envelope, which is commonly thought to act as a repressive environment for gene expression, does not appear to play a major role. We show that position effects, which have been shown for artificially lamina-targeted genes, also exist for endogenous loci and consider the possible biological relevance of the observed small effect.

molecular biology↗

bioRxiv2021

Genome-wide association study of gastric cancer- and duodenal ulcer-derived Helicobacter pylori strains reveals discriminatory amino acid differences and novel oncoprotein candidates

Genome-wide association studies (GWASs) can reveal genetic variations associated with a phenotype in the absence of any hypothesis of candidate genes. The problem of false-positive sites linked with the responsible site might be bypassed in bacteria with a high homologous recombination rate, such as Helicobacter pylori, which causes gastric cancer (GC). We conducted a GWAS followed by regression-based prediction of GC and duodenal ulcer H. pylori strains. We identified 14 single nucleotide polymorphisms (11 amino acid changes) that, combined, allowed effective disease discrimination. They were often informative of the underlying molecular mechanisms, such as electric charge alteration at the ligand-binding pocket, alteration in subunit interaction, and mode-switching of DNA methylation. We also identified three novel virulence factors/oncoprotein candidates. These results provide both defined targets for further informatic and experimental analyses to gain insights into GC pathogenesis and a basis for identifying a set of biomarkers for application in clinical settings.

physiology↗

bioRxiv2020

A spontaneous genetically-induced epiallele at a retrotransposon shapes host genome function

Intracisternal A-particles (IAPs) are endogenous retroviruses (ERVs) responsible for most insertional mutations in the mouse. Full-length IAPs harbour genes flanked by long terminal repeats (LTRs). Here, we identify a solo LTR IAP variant (C57iap1solo) recently formed in the inbred C57BL/6J mouse strain. In contrast to the C57BL/6J full-length IAP at this locus (C57iap1full), C57iap1solo lacks DNA methylation and H3K9 trimethylation. The distinct DNA methylation levels between the two alleles are established during preimplantation development, likely due to loss of KRAB zinc finger protein binding at the C57iap1solo variant. C57iap1solo methylation increases and becomes more variable in a hybrid genetic background yet is unresponsive to maternal dietary methyl supplementation. Differential epigenetic modification of the two variants is associated with metabolic differences and tissue-specific changes in adjacent gene expression. Our characterisation of C57iap1 as a genetically-induced epiallele with functional consequences establishes a new model to study transposable element repression and host-element co-evolution.

genetics↗

bioRxiv2020

DNA damage inhibits root growth by enhancing cytokinin biosynthesis in Arabidopsis thaliana.

Plant root growth is influenced by external factors to adapt to changing environmental conditions. However, the mechanisms by which environmental stresses affect root growth remain elusive. Here we found that DNA double-strand breaks (DSBs) induce the expression of genes for the synthesis of cytokinin hormones and enhance the accumulation of cytokinins in the Arabidopsis root tip. This is a programmed response to DSBs through the DNA damage signaling pathway. Our data showed that activation of cytokinin signalling suppresses the expression of PIN-FORMED genes that encode efflux carriers of another plant hormone, auxin, thereby disturbing downward auxin flow and causing cell cycle retardation in the G2 phase. Elevated cytokinin signalling also promotes an early transition from cell division to endoreplication, resulting in a reduction of the root meristem size. We propose that in response to DNA stress, plants inhibit root growth by orchestrating hormone biosynthesis and signalling.

plant biology↗