Redox Regulation of Phosphatase and Tensin Homolog by Bicarbonate and Hydrogen Peroxide: Implication of Peroxymonocarbonate in Cell Signaling.

Phosphatase and tensin homolog (PTEN) is a negative regulator of the phosphoinositide 3-kinases/protein kinase B (PI3K/AKT) signaling pathway. Notably, its active site contains a cysteine residue that is susceptible to oxidation by hydrogen peroxide (H2O2). This oxidation inhibits the phosphatase function of PTEN, critically contributing to the activation of the PI3K/AKT pathway. Upon the stimulation of cell surface receptors, the activity of NADPH oxidase (NOX) generates a transient amount of H2O2, serving as a mediator in this pathway by oxidizing PTEN. The mechanism underlying this oxidation, occurring despite the presence of highly efficient and abundant cellular oxidant-protecting and reducing systems, continues to pose a perplexing conundrum. Here, we demonstrate that the presence of bicarbonate (HCO3-) promoted the rate of H2O2-mediated PTEN oxidation, probably through the formation of peroxymonocarbonate (HCO4-), and consequently potentiated the phosphorylation of AKT. Acetazolamide (ATZ), a carbonic anhydrase (CA) inhibitor, was shown to diminish the oxidation of PTEN. Thus, CA can also be considered as a modulator in this context. In essence, our findings consolidate the crucial role of HCO3- in the redox regulation of PTEN by H2O2, leading to the presumption that HCO4- is a signaling molecule during cellular physiological processes.

Aerosol-Synthesized Surfactant-Free Single-Walled Carbon Nanotube-Based NO2 Sensors: Unprecedentedly High Sensitivity and Fast Recovery.

This study pioneers a chemical sensor based on surfactant-free aerosol-synthesized single-walled carbon nanotube (SWCNT) films for detecting nitrogen dioxide (NO2). Unlike conventional CNTs, the SWCNTs used in this study exhibit one of the highest surface-to-volume ratios. They show minimal bundling without the need for surfactants and have the lowest number of defects among reported CNTs. Furthermore, the dry-transferrable and facile one-step lamination results in promising industrial viability. When applied to devices, the sensor shows excellent sensitivity (41.6% at 500 ppb), rapid response/recovery time (14.2/120.8 s), a remarkably low limit of detection (below ≈0.161 ppb), minimal noise, repeatability for more than 50 cycles without fluctuation, and long-term stability for longer than 6 months. This is the best performance reported for a pure CNT-based sensor. In addition, the aerosol SWCNTs demonstrate consistent gas-sensing performance even after 5000 bending cycles, indicating their suitability for wearable applications. Based on experimental and theoretical analyses, the proposed aerosol CNTs are expected to overcome the limitations associated with conventional CNT-based sensors, thereby offering a promising avenue for various sensor applications.

QuadST: A Powerful and Robust Approach for Identifying Cell-Cell Interaction-Changed Genes on Spatially Resolved Transcriptomics.

Spatially resolved transcriptomics (SRT) have enabled profiling spatial organization of cells and their transcriptome in situ. Various analytical methods have been developed to uncover cell-cell interaction processes using SRT data. To improve upon existing efforts, we developed a novel statistical framework called QuadST for the robust and powerful identification of interaction-changed genes (ICGs) for cell-type-pair specific interactions on a single-cell SRT dataset. QuadST is motivated by the idea that in the presence of cell-cell interaction, gene expression level can vary with cell-cell distance between cell type pairs, which can be particularly pronounced within and in the vicinity of cell-cell interaction distance. Specifically, QuadST infers ICGs in a specific cell type pair's interaction based on a quantile regression model, which allows us to assess the strength of distance-expression association across entire distance quantiles conditioned on gene expression level. To identify ICGs, QuadST performs a hypothesis testing with an empirically estimated FDR, whose upper bound is determined by the ratio of cumulative associations at symmetrically smaller and larger distance quantiles simultaneously across all genes. Simulation studies illustrate that QuadST provides consistent FDR control and better power performance than other compared methods. Its application on SRT datasets profiled from mouse brains demonstrates that QuadST can identify ICGs presumed to play a role in specific cell type pair interactions (e.g., synaptic pathway genes among excitatory neuron cell interactions). These results suggest that QuadST can be a useful tool to discover genes and regulatory processes involved in specific cell type pair interactions.

Transcriptomic taxonomy and neurogenic trajectories of adult human, macaque, and pig hippocampal and entorhinal cells.

The hippocampal-entorhinal system supports cognitive functions, has lifelong neurogenic capabilities in many species, and is selectively vulnerable to Alzheimer's disease. To investigate neurogenic potential and cellular diversity, we profiled single-nucleus transcriptomes in five hippocampal-entorhinal subregions in humans, macaques, and pigs. Integrated cross-species analysis revealed robust transcriptomic and histologic signatures of neurogenesis in the adult mouse, pig, and macaque but not humans. Doublecortin (DCX), a widely accepted marker of newly generated granule cells, was detected in diverse human neurons, but it did not define immature neuron populations. To explore species differences in cellular diversity and implications for disease, we characterized subregion-specific, transcriptomically defined cell types and transitional changes from the three-layered archicortex to the six-layered neocortex. Notably, METTL7B defined subregion-specific excitatory neurons and astrocytes in primates, associated with endoplasmic reticulum and lipid droplet proteins, including Alzheimer's disease-related proteins. This resource reveals cell-type- and species-specific properties shaping hippocampal-entorhinal neurogenesis and function.

Multi-Walled Carbon Nanotube-Assisted Encapsulation Approach for Stable Perovskite Solar Cells.

Perovskite solar cells (PSCs) are regarded as the next-generation thin-film energy harvester, owing to their high performance. However, there is a lack of studies on their encapsulation technology, which is critical for resolving their shortcomings, such as their degradation by oxygen and moisture. It is determined that the moisture intrusion and the heat trapped within the encapsulating cover glass of PSCs influenced the operating stability of the devices. Therefore, we improved the moisture and oxygen barrier ability and heat releasing capability in the passivation of PSCs by adding multi-walled carbon nanotubes to the epoxy resin used for encapsulation. The 0.5 wt% of carbon nanotube-added resin-based encapsulated PSCs exhibited a more stable operation with a ca. 30% efficiency decrease compared to the ca. 63% decrease in the reference devices over one week under continuous operation. Specifically, the short-circuit current density and the fill factor, which are affected by moisture and oxygen-driven degradation, as well as the open-circuit voltage, which is affected by thermal damage, were higher for the multi-walled carbon nanotube-added encapsulated devices than the control devices, after the stability test.

Whole-Genome and RNA Sequencing Reveal Variation and Transcriptomic Coordination in the Developing Human Prefrontal Cortex.

Gene expression levels vary across developmental stage, cell type, and region in the brain. Genomic variants also contribute to the variation in expression, and some neuropsychiatric disorder loci may exert their effects through this mechanism. To investigate these relationships, we present BrainVar, a unique resource of paired whole-genome and bulk tissue RNA sequencing from the dorsolateral prefrontal cortex of 176 individuals across prenatal and postnatal development. Here we identify common variants that alter gene expression (expression quantitative trait loci [eQTLs]) constantly across development or predominantly during prenatal or postnatal stages. Both "constant" and "temporal-predominant" eQTLs are enriched for loci associated with neuropsychiatric traits and disorders and colocalize with specific variants. Expression levels of more than 12,000 genes rise or fall in a concerted late-fetal transition, with the transitional genes enriched for cell-type-specific genes and neuropsychiatric risk loci, underscoring the importance of cataloging developmental trajectories in understanding cortical physiology and pathology.

Organic/Inorganic Hybrid Buffer in InGaZnO Transistors under Repetitive Bending Stress for High Electrical and Mechanical Stability.

We investigated the influence of the multilayered hybrid buffer consisting of Al2O3/PA (polyacrylic) organic layer/Al2O3 on the electrical and mechanical properties of amorphous InGaZnO (a-IGZO) thin-film transistors (TFTs). The multilayered organic/inorganic hybrid buffer has multiple beneficial effects on the flexible TFTs under repetitive bending stress. First, compared to the PA or Al2O3 single-layered buffer, the multilayered hybrid buffer showed an improved WVTR value of 1.1 × 10-4 g/m2 day. Even after 40,000 bending cycles, the WVTR value of the hybrid buffer increased only by 17%, while the WVTR value of the Al2O3 layer doubled after cyclical bending stress. We also confirmed that the hybrid buffer has advantages in mechanical durability of the TFT layers because of the change in the position of the neutral plane and the strain reduction effect by the PA organic layer. When we fabricate a top-gate a-IGZO TFT with the hybrid buffer layer (HB TFT), the device shows Vth = 0.74 V, µFE = 14.4 cm2/V·s, a subthreshold slope of 0.27 V/dec, and hysteresis of 0.21 V, which are superior to that of TFTs fabricated on an Al2O3 single-layer buffer (IB TFT). From the X-ray photoelectron spectroscopy and elastic recoil detection analysis, the difference in the electrical performance of TFTs could be explained by hydrogen-related molecules. After annealing at 270 °C, the amounts of hydrogen found in the a-IGZO layer for the IB, HB, and OB TFTs were 3.57 × 1021, 5.77 × 1021, and 7.34 × 1021 atoms/cm3, respectively. A top-gate bottom-contact structured a-IGZO TFT fabricated on the PA layer (OB TFT) showed a gate dielectric breakdown because of excessively high hydrogen content and high nonbonding oxygen content. On the other hand, HB TFTs showed better positive bias stability because of the higher hydrogen concentration, as hydrogen (when not excessive) is beneficial in passivating electron traps. Finally, we conducted 60,000 repetitive bending cycles on IB TFTs and HB TFTs with various bending radii down to 1.5 mm. The HB TFT shows improved mechanical durability and exhibits less electrical degradation during and after repetitive bending stress, compared to the IB TFT.

Enhancing Radiotherapeutic Effect With Nanoparticle-Mediated Radiosensitizer Delivery Guided By Focused Gamma Rays In Lewis Lung Carcinoma-Bearing Mouse Brain Tumor Models.

BACKGROUND: Targeting radiosensitizer-incorporated nanoparticles to a tumor could allow for less normal tissue toxicity with more efficient drug release, thus improving the efficacy and safety of radiation treatment. The aim of this study was to improve tumor-specific delivery and bioavailability of a nanoparticle-mediated radiosensitizer in mouse brain tumor models. METHODS: A pH-sensitive nanoparticle, chitoPEGAcHIS, was conjugated to recombinant peptide HVGGSSV that could bind to tax-interaction protein 1 (TIP-1) as a radiation-inducible receptor. Then the c-Jun N-terminal kinase (JNK) inhibitor, SP600125 was incorporated into this copolymer to fabricate a HVGGSSV-chitoPEGAcHIS-SP600125 (HVSP-NP) nanoradiosensitizer. In vitro and in vivo radiation treatment were performed using a Gamma Knife unit. The tumor targetability of HVSP-NP was estimated by optical bioluminescence. Synergistic therapeutic effects of radiation treatment and HVSP-NP were investigated in Lewis lung carcinoma (LLC) cell-bearing mouse brain tumor models. RESULTS: The SP600125 JNK inhibitor effectively reduced DNA damage repair to irradiated LLC cells. A pH sensitivity assay indicated that HVSP-NP swelled at acidic pH and increased in diameter, and its release rate gradually increased. Optical bioluminescence assay showed that radiation induced TIP-1 expression in mouse brain tumor and that the nanoradiosensitizer selectively targeted irradiated tumors. Radiation treatment with HVSP-NP induced greater apoptosis and significantly inhibited tumor growth compared to radiation alone. CONCLUSION: As a novel nanoradiosensitizer, HVSP-NP was found to be able to selectively target irradiated tumors and significantly increase tumor growth delay in LLC-bearing mouse brain tumor models. This research shows that delivering a pH-sensitive nanoradiosensitizer to a brain tumor in which TIP-1 is induced by radiation can result in improved radiosensitizer-release in an acidic microenvironment of tumor tissue and in created synergistic effects in radiation treatment.

Integrative functional genomic analysis of human brain development and neuropsychiatric risks.

To broaden our understanding of human neurodevelopment, we profiled transcriptomic and epigenomic landscapes across brain regions and/or cell types for the entire span of prenatal and postnatal development. Integrative analysis revealed temporal, regional, sex, and cell type-specific dynamics. We observed a global transcriptomic cup-shaped pattern, characterized by a late fetal transition associated with sharply decreased regional differences and changes in cellular composition and maturation, followed by a reversal in childhood-adolescence, and accompanied by epigenomic reorganizations. Analysis of gene coexpression modules revealed relationships with epigenomic regulation and neurodevelopmental processes. Genes with genetic associations to brain-based traits and neuropsychiatric disorders (including MEF2C, SATB2, SOX5, TCF4, and TSHZ3) converged in a small number of modules and distinct cell types, revealing insights into neurodevelopment and the genomic basis of neuropsychiatric risks.

The 7q11.23 Protein DNAJC30 Interacts with ATP Synthase and Links Mitochondria to Brain Development.

Despite the known causality of copy-number variations (CNVs) to human neurodevelopmental disorders, the mechanisms behind each gene's contribution to the constellation of neural phenotypes remain elusive. Here, we investigated the 7q11.23 CNV, whose hemideletion causes Williams syndrome (WS), and uncovered that mitochondrial dysfunction participates in WS pathogenesis. Dysfunction is facilitated in part by the 7q11.23 protein DNAJC30, which interacts with mitochondrial ATP-synthase machinery. Removal of Dnajc30 in mice resulted in hypofunctional mitochondria, diminished morphological features of neocortical pyramidal neurons, and altered behaviors reminiscent of WS. The mitochondrial features are consistent with our observations of decreased integrity of oxidative phosphorylation supercomplexes and ATP-synthase dimers in WS. Thus, we identify DNAJC30 as an auxiliary component of ATP-synthase machinery and reveal mitochondrial maladies as underlying certain defects in brain development and function associated with WS.

Large-Scale trans-eQTLs Affect Hundreds of Transcripts and Mediate Patterns of Transcriptional Co-regulation.

Efforts to decipher the causal relationships between differences in gene regulation and corresponding differences in phenotype have been stymied by several basic technical challenges. Although detecting local, cis-eQTLs is now routine, trans-eQTLs, which are distant from the genes of origin, are far more difficult to find because millions of SNPs must currently be compared to thousands of transcripts. Here, we demonstrate an alternative approach: we looked for SNPs associated with the expression of many genes simultaneously and found that hundreds of trans-eQTLs each affect hundreds of transcripts in lymphoblastoid cell lines across three African populations. These trans-eQTLs target the same genes across the three populations and show the same direction of effect. We discovered that target transcripts of a high-confidence set of trans-eQTLs encode proteins that interact more frequently than expected by chance, are bound by the same transcription factors, and are enriched for pathway annotations indicative of roles in basic cell homeostasis. We thus demonstrate that our approach can uncover trans-acting transcriptional control circuits that affect co-regulated groups of genes: a key to understanding how cellular pathways and processes are orchestrated.

Network Analysis of Genome-Wide Selective Constraint Reveals a Gene Network Active in Early Fetal Brain Intolerant of Mutation.

Using robust, integrated analysis of multiple genomic datasets, we show that genes depleted for non-synonymous de novo mutations form a subnetwork of 72 members under strong selective constraint. We further show this subnetwork is preferentially expressed in the early development of the human hippocampus and is enriched for genes mutated in neurological Mendelian disorders. We thus conclude that carefully orchestrated developmental processes are under strong constraint in early brain development, and perturbations caused by mutation have adverse outcomes subject to strong purifying selection. Our findings demonstrate that selective forces can act on groups of genes involved in the same process, supporting the notion that purifying selection can act coordinately on multiple genes. Our approach provides a statistically robust, interpretable way to identify the tissues and developmental times where groups of disease genes are active.

Changes in T-cell subsets identify responders to FcR-nonbinding anti-CD3 mAb (teplizumab) in patients with type 1 diabetes.

The mechanisms whereby immune therapies affect progression of type 1 diabetes (T1D) are not well understood. Teplizumab, an FcR nonbinding anti-CD3 mAb, has shown efficacy in multiple randomized clinical trials. We previously reported an increase in the frequency of circulating CD8(+) central memory (CD8CM) T cells in clinical responders, but the generalizability of this finding and the molecular effects of teplizumab on these T cells have not been evaluated. We analyzed data from two randomized clinical studies of teplizumab in patients with new- and recent-onset T1D. At the conclusion of therapy, clinical responders showed a significant reduction in circulating CD4(+) effector memory T cells. Afterward, there was an increase in the frequency and absolute number of CD8CM T cells. In vitro, teplizumab expanded CD8CM T cells by proliferation and conversion of non-CM T cells. Nanostring analysis of gene expression of CD8CM T cells from responders and nonresponders versus placebo-treated control subjects identified decreases in expression of genes associated with immune activation and increases in expression of genes associated with T-cell differentiation and regulation. We conclude that CD8CM T cells with decreased activation and regulatory gene expression are associated with clinical responses to teplizumab in patients with T1D.

Rosiglitazone reduces tau phosphorylation via JNK inhibition in the hippocampus of rats with type 2 diabetes and tau transfected SH-SY5Y cells.

Increasing evidence supports an association between Alzheimer's disease (AD) and diabetes. Rosiglitazone, a peroxisome proliferator-activated receptor-γ (PPARγ) agonist, which is an anti-diabetic agent against type 2 diabetes, is currently in Phase III clinical trials in AD patients because rosiglitazone reduces ß-amyloid (Aß) pathology and inflammation. However, few studies have investigated whether rosiglitazone affects tau phosphorylation, another critical pathological feature of AD. Thus, we investigated it using OLETF type 2 diabetic rats and streptozotocin-injected type 1 diabetic mice. Interestingly, rosiglitazone reduced tau phosphorylation only in the hippocampus of OLETF type 2 diabetes rats, and not in that of STZ-injected type 1 diabetes mice. The activity of JNK was reduced in the hippocampus of rosiglitazone-treated OLETF rats, correlating with a reduction in tau phosphorylation, however, which was not correlated with GSK3ß activity. In human tau-transfected SH-SY5Y neuronal cell line, reduction of tau phosphorylation was also associated with reduction of JNK activity, not of GSK3ß activity. Hence, rosiglitazone could be used in reducing tau phosphorylation through JNK inactivation for therapeutic effects in type 2 diabetes related Alzheimer's disease.