Innate immune sensing and signaling of cytosolic nucleic acids.

The innate immune system utilizes pattern-recognition receptors (PRRs) to detect the invasion of pathogens and initiate host antimicrobial responses such as the production of type I interferons and proinflammatory cytokines. Nucleic acids, which are essential genetic information carriers for all living organisms including viral, bacterial, and eukaryotic pathogens, are major structures detected by the innate immune system. However, inappropriate detection of self nucleic acids can result in autoimmune diseases. PRRs that recognize nucleic acids in cells include several endosomal members of the Toll-like receptor family and several cytosolic sensors for DNA and RNA. Here, we review the recent advances in understanding the mechanism of nucleic acid sensing and signaling in the cytosol of mammalian cells as well as the emerging role of cytosolic nucleic acids in autoimmunity.

CREAMMIST: an integrative probabilistic database for cancer drug response prediction.

Extensive in vitro cancer drug screening datasets have enabled scientists to identify biomarkers and develop machine learning models for predicting drug sensitivity. While most advancements have focused on omics profiles, cancer drug sensitivity scores precalculated by the original sources are often used as-is, without consideration for variabilities between studies. It is well-known that significant inconsistencies exist between the drug sensitivity scores across datasets due to differences in experimental setups and preprocessing methods used to obtain the sensitivity scores. As a result, many studies opt to focus only on a single dataset, leading to underutilization of available data and a limited interpretation of cancer pharmacogenomics analysis. To overcome these caveats, we have developed CREAMMIST (https://creammist.mtms.dev), an integrative database that enables users to obtain an integrative dose-response curve, to capture uncertainty (or high certainty when multiple datasets well align) across five widely used cancer cell-line drug-response datasets. We utilized the Bayesian framework to systematically integrate all available dose-response values across datasets (>14 millions dose-response data points). CREAMMIST provides easy-to-use statistics derived from the integrative dose-response curves for various downstream analyses such as identifying biomarkers, selecting drug concentrations for experiments, and training robust machine learning models.

Upconversion Nanoparticles Based Sensing: From Design to Point-of-Care Testing.

Rare earth-doped upconversion nanoparticles (UCNPs) have achieved a wide range of applications in the sensing field due to their unique anti-Stokes luminescence property, minimized background interference, excellent biocompatibility, and stable physicochemical properties. However, UCNPs-based sensing platforms still face several challenges, including inherent limitations from UCNPs such as low quantum yields and narrow absorption cross-sections, as well as constraints related to energy transfer efficiencies in sensing systems. Therefore, the construction of high-performance UCNPs-based sensing platforms is an important cornerstone for conducting relevant research. This work begins by providing a brief overview of the upconversion luminescence mechanism in UCNPs. Subsequently, it offers a comprehensive summary of the sensors' types, design principles, and optimized design strategies for UCNPs sensing platforms. More cost-effective and promising point-of-care testing applications implemented based on UCNPs sensing systems are also summarized. Finally, this work addresses the future challenges and prospects for UCNPs-based sensing platforms.

circSORBS1 inhibits lung cancer progression by sponging miR-6779-5p and directly binding RUFY3 mRNA.

Lung cancer is the primary cause of cancer-related death worldwide, and its global incidence and mortality rates remain high. The differential expression of circular RNAs (circRNAs) can affect the development of cancer, but the mechanisms by which circRNAs regulate lung cancer progression remain unclear. In this study, we identified circSORBS1, a circRNA that has not been previously described in lung cancer and is significantly underexpressed in lung cancer tissues, blood and cell lines, and the low expression of circSORBS1 correlated with tumour grade and prognosis. In vitro and in vivo functional experiments revealed that circSORBS1 overexpression inhibited cell proliferation and migration while enhancing apoptosis. Mechanistically, circSORBS1 acts as a sponge for miR-6779-5p, indirectly inhibiting RUFY3 mRNA degradation. Simultaneously, it binds to RUFY3 mRNA to enhance its stability. This dual regulatory mechanism leads to an increase in RUFY3 protein levels, which ultimately activates the YWHAE/BAD/BCL2 apoptotic signalling pathway and suppresses lung cancer progression. Our findings not only increase the knowledge about the regulatory pattern of circRNA expression but also provide new insights into the mechanisms by which circRNAs regulate lung cancer development.

Light Conversion Nanomaterials for Wireless Phototherapy.

Phototherapy including optogenetics, photodynamic therapy (PDT), photothermal therapy (PTT), and photoimmunotherapy (PIT) has been proven to be effective against different diseases. However, as the name suggests, phototherapy requires light irradiation, thus its therapeutic efficiency is often restricted by limited depth of light penetration within biological tissue. This light penetration limitation is significantly adverse to PDT and optogenetics because both therapies are usually activated with UV and visible light of very poor tissue penetration efficiency. Current light delivery methods usually involve cumbersome setups and require optical fiber or catheter insertion, which not only restrict the movement of patients but also impose incompatibility issues with chronic implantation. To address the existing challenges, wireless phototherapy was developed through various approaches over recent years, which usually relies on implantable wireless electronic devices. However, the application of wireless electronic devices is limited by invasion during implantation, unwanted heat generation, and adverse immunogenicity of these devices.Over the recent years, applying light conversion nanomaterials as light transducers for wireless phototherapy has garnered much interest. Compared with implantable electronic devices and optical fiber, nanomaterials can be easily injected into the body with minimal invasiveness and can also be surface functionalized to increase their biocompatibility and cell accumulation efficiency. Commonly applied light conversion nanomaterials include upconversion nanoparticles (UCNPs), X-ray nanoscintillators, and persistent luminescence nanoparticles (PLNPs). UCNPs and X-ray nanoscintillators can respectively convert near-infrared (NIR) light and X-ray, which have good tissue penetration efficiency, to UV or visible light, which is suitable for activating phototherapy. PLNPs can be excited by external light such as X-rays and NIR light and retain long afterglow luminescence after the removal of the excitation light source. As a result, applying PLNPs in phototherapy can potentially reduce irradiation time from external light sources, thus minimizing tissue photodamage. This Account aims to briefly discuss (i) the mechanisms of different phototherapies, (ii) the development and mechanisms of light conversion nanomaterials, (iii) the application of light conversion nanomaterials in wireless phototherapy, highlighting how they relieve current challenges in phototherapy, and (iv) perspectives for future development of light conversion nanomaterials for wireless phototherapy.

Splenic Dendritic Cells Survey Red Blood Cells for Missing Self-CD47 to Trigger Adaptive Immune Responses.

Sheep red blood cells (SRBCs) have long been used as a model antigen for eliciting systemic immune responses, yet the basis for their adjuvant activity has been unknown. Here, we show that SRBCs failed to engage the inhibitory mouse SIRPα receptor on splenic CD4(+) dendritic cells (DCs), and this failure led to DC activation. Removal of the SIRPα ligand, CD47, from self-RBCs was sufficient to convert them into an adjuvant for adaptive immune responses. DC capture of Cd47(-/-) RBCs and DC activation occurred within minutes in a Src-family-kinase- and CD18-integrin-dependent manner. These findings provide an explanation for the adjuvant mechanism of SRBCs and reveal that splenic DCs survey blood cells for missing self-CD47, a process that might contribute to detecting and mounting immune responses against pathogen-infected RBCs.

Health Messaging Strategies for Vaping Prevention and Cessation Among Youth and Young Adults: A Systematic Review.

This systematic review evaluates health messaging strategies for the prevention and cessation of e-cigarette use among youth and young adults. Health messaging strategies were defined as the strategic process of developing messages with the intent to shape, reinforce, or change recipients' health attitudes and behaviors. McGuire's Communication/Persuasion Model guided the analysis of the messaging strategies, focusing on the model's five communication inputs (i.e. source, message, channel, audience, destination) and 14 persuasive outcomes. Nine databases were searched from January 2007 to September 2023. The inclusion criteria encompassed studies in English that presented quantitative data on messaging strategies aimed at discouraging vaping among youth and young adults. Each study was also coded for study characteristics and the utilization of theory. Out of 6,045 studies, 25 met the inclusion criteria. The reviewed studies exhibit a diverse array of research methods and a consistent integration of theories. The review emphasizes the nuanced main and interaction effects of various communication inputs, such as message features and audience characteristics, while also pointing out a research gap in message sources. In addition, the utilization of social media for effective messaging to engage the audience requires further research. Only one study specifically evaluated messaging strategies for vaping cessation. More research is imperative to develop targeted and tailored messages that effectively prevent and reduce vaping, especially among populations at higher risk of vaping-related harms, while also leveraging effective channels and innovative communication technologies to engage the audience.

Exploring ways to improve China's ecological well-being amidst air pollution challenges using mixed methods.

Ecological well-being performance (EWP), a novel concept in sustainable development research, diverges from traditional ecological efficiency in terms of perspectives, core content, and driving factors. However, research on EWP remains insufficiently comprehensive, particularly the corresponding theoretical and methodological investigations into driving pathways. To address this gap, this study develops an "economy-environment-health" framework, incorporating air pollution and associated health losses into the evaluation system, and employs a two-stage Super-NSBM and Window DEA model for reevaluating EWP. The study further investigates the primary pathways of EWP, focusing on environmental regulations, technological innovation, and structural adjustments through both quantitative and qualitative methods. Quantitative spatial econometric analysis reveals that factors such as market-driven environmental regulations, green invention patents, and industrial and energy consumption structures significantly enhance EWP. While examining the "net effects" contributions of individual variables using spatial econometric models, the fsQCA method is employed to identify four effective driving paths for EWP from a configurational perspective. These paths are 1) technological innovation and structural adjustment under environmental regulations with public participation; 2) a combination of environmental regulation, technological innovation, and structural adjustment; 3) structural adjustment with minimal influence from environmental regulations and technological innovation; and 4) structural adjustment directed by market-incentive environmental regulations.

An Argonaute phosphorylation cycle promotes microRNA-mediated silencing.

MicroRNAs (miRNAs) perform critical functions in normal physiology and disease by associating with Argonaute proteins and downregulating partially complementary messenger RNAs (mRNAs). Here we use clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated protein 9 (Cas9) genome-wide loss-of-function screening coupled with a fluorescent reporter of miRNA activity in human cells to identify new regulators of the miRNA pathway. By using iterative rounds of screening, we reveal a novel mechanism whereby target engagement by Argonaute 2 (AGO2) triggers its hierarchical, multi-site phosphorylation by CSNK1A1 on a set of highly conserved residues (S824-S834), followed by rapid dephosphorylation by the ANKRD52-PPP6C phosphatase complex. Although genetic and biochemical studies demonstrate that AGO2 phosphorylation on these residues inhibits target mRNA binding, inactivation of this phosphorylation cycle globally impairs miRNA-mediated silencing. Analysis of the transcriptome-wide binding profile of non-phosphorylatable AGO2 reveals a pronounced expansion of the target repertoire bound at steady-state, effectively reducing the active pool of AGO2 on a per-target basis. These findings support a model in which an AGO2 phosphorylation cycle stimulated by target engagement regulates miRNA:target interactions to maintain the global efficiency of miRNA-mediated silencing.

Moralization of E-cigarette Use and Regulation: A Mixed-Method Computational Analysis of Opinion Polarization.

E-cigarette use, or vaping, is undergoing a process of moralization in which issues about vaping evolve from being morally neutral to having discernible moral implications. Using Moral Foundations Theory, this study compared the moral narratives underlying polarized views about e-cigarette use and regulation. We integrated computational and human strategies by conducting the Chow test on the time series data and classification, topic modeling, and Chi-square tests on posts (N = 2,669) from 26 pro-vaping and 19 anti-vaping Facebook Pages. The observation period (August 1, 2019 to March 5, 2020) encompassed the outbreak of "e-cigarette or vaping product use associated lung injury" (EVALI), deaths and subsequent legislation. Results revealed that pro-vaping posts were more likely than anti-vaping posts to mention Fairness/cheating and Authority/subversion, involving a conspiracy belief in an "e-cigarettes vs. Big Tobacco" rivalry, while anti-vaping posts were more likely to mention Sanctity/degradation. There were no significant differences between pro-vaping and anti-vaping posts in the likelihood of mentioning Care/harm or Loyalty/betrayal. Nevertheless, according to the topic modeling results, the use of moral foundations varied between pro-vaping and anti-vaping narratives, with the meanings of Care/harm and Loyalty/betrayal dependent on the post author's group affiliation. Health interventions can tailor persuasive messages to different moral values and debunk misinformation about public health policies to mitigate the vaping epidemic. Theoretical implications are also discussed.

TFEB, a master regulator of autophagy and biogenesis, unexpectedly promotes apoptosis in response to the cyclopentenone prostaglandin 15d-PGJ2.

Transcriptional factor EB (TFEB), a master regulator of autophagy and lysosomal biogenesis, is generally regarded as a pro-survival factor. Here, we identify that besides its effect on autophagy induction, TFEB exerts a pro-apoptotic effect in response to the cyclopentenone prostaglandin 15-deoxy-∆-12,14-prostaglandin J2 (15d-PGJ2). Specifically, 15d-PGJ2 promotes TFEB translocation from the cytoplasm into the nucleus to induce autophagy and lysosome biogenesis via reactive oxygen species (ROS) production rather than mTORC1 inactivation. Surprisingly, TFEB promotes rather than inhibits apoptosis in response to 15d-PGJ2. Mechanistically, ROS-mediated TFEB translocation into the nucleus transcriptionally upregulates the expression of ATF4, which is required for apoptosis elicited by 15d-PGJ2. Additionally, inhibition of TFEB activation by ROS scavenger N-acetyl cysteine or inhibition of protein synthesis by cycloheximide effectively compromises ATF4 upregulation and apoptosis in response to 15d-PGJ2. Collectively, these results indicate that ROS-induced TFEB activation exerts a novel role in promoting apoptosis besides its role in regulating autophagy in response to 15d-PGJ2. This work not only evidences how TFEB is activated by 15d-PGJ2, but also unveils a previously unexplored role of ROS-dependent activation of TFEB in modulating cell apoptosis in response to 15d-PGJ2.

Cyclic GMP-AMP containing mixed phosphodiester linkages is an endogenous high-affinity ligand for STING.

The presence of microbial or self DNA in the cytoplasm of mammalian cells is a danger signal detected by the DNA sensor cyclic-GMP-AMP (cGAMP) synthase (cGAS), which catalyzes the production of cGAMP that in turn serves as a second messenger to activate innate immune responses. Here we show that endogenous cGAMP in mammalian cells contains two distinct phosphodiester linkages, one between 2'-OH of GMP and 5'-phosphate of AMP, and the other between 3'-OH of AMP and 5'-phosphate of GMP. This molecule, termed 2'3'-cGAMP, is unique in that it binds to the adaptor protein STING with a much greater affinity than cGAMP molecules containing other combinations of phosphodiester linkages. The crystal structure of STING bound to 2'3'-cGAMP revealed the structural basis of this high-affinity binding and a ligand-induced conformational change in STING that may underlie its activation.

Critical role of integrin CD11c in splenic dendritic cell capture of missing-self CD47 cells to induce adaptive immunity.

CD11c, also known as integrin alpha X, is the most widely used defining marker for dendritic cells (DCs). CD11c can bind complement iC3b and mediate phagocytosis in vitro, for which it is also referred to as complement receptor 4. However, the functions of this prominent marker protein in DCs, especially in vivo, remain poorly defined. Here, in the process of studying DC activation and immune responses induced by cells lacking self-CD47, we found that DC capture of CD47-deficient cells and DC activation was dependent on the integrin-signaling adaptor Talin1. Specifically, CD11c and its partner Itgb2 were required for DC capture of CD47-deficient cells. CD11b was not necessary for this process but could partially compensate in the absence of CD11c. Mice with DCs lacking Talin1, Itgb2, or CD11c were defective in supporting T-cell proliferation and differentiation induced by CD47-deficient cell associated antigen. These findings establish a critical role for CD11c in DC antigen uptake and activation in vivo. They may also contribute to understanding the functional mechanism of CD47-blockade therapies.

Mechanical stretch activates glycometabolism-related enzymes via estrogen in C2 C12 myoblasts.

Moderate exercise improves glycometabolic disorder and type 2 diabetes mellitus in menopausal females. So far, the effect of exercise-induced estrogen on muscular glycometabolism is not well defined. The current study was designed to explore the effect of mechanical stretch-induced estrogen on glycometabolism in mouse C2 C12 myoblasts. The mouse C2 C12 myoblasts in vitro were assigned randomly to the control (C), stretch (S), and stretch plus aromatase inhibitor anastrozole (SA) groups. Cells in the S group were stretched by the Flexcell FX-5000™ system (15% magnitude, 1 Hz frequency, and 6-hr duration) whereas those in the SA group were treated with 400 µg/ml anastrozole before the same stretching. Glucose uptake, estradiol levels, PFK-1 levels, and oxygen consumption rate were determined, and the expression of HK, PI3K, p-AKT, AKT, and GLUT4 proteins were semiquantified with western blot analysis. Compared to the control, the estradiol level, oxygen consumption rate, expression of HK, PI3K, and PFK-1 proteins, the ratio of p-AKT to AKT, and the ratio of GLUT4 in the cell membrane to that in the whole cell were higher in the S group. On the other hand, the estradiol level, glucose uptake, expression of PFK-1 and GLUT4 proteins, oxygen consumption rate, expression of HK protein, and the ratio of p-AKT/AKT were lower in the myoblasts in the SA group than those in the S group. The level of estradiol was positively correlated with glucose uptake (p < .01, r = .818). Therefore, mechanical stretch-induced estrogen increased the expression of glycometabolism-related enzymes and proteins in the mouse C2 C12 myoblasts.

Characterization of in vitro neural functional connectivity on a neurofluidic device.

Understanding the mechanism of functional connectivity in neural system is of great benefit to lot of researches and applications. Microfluidics and microelectrode arrays (MEAs) have been frequently utilized for in vitro neural cultures study. However, there are few studies on the functional connectivity of neural cultures grown on a microfluidic chip. It is intriguing to unveil the influences of microfluidic structures on in vitro neuronal networks from the perspective of functional connectivity. Hence, in the present study, a device was established, which comprised a microfluidic chamber for cell growth and a MEA substrate for recording the electrophysiological response of the neuronal networks. The network topology, neural firing rate, neural bursting rate and network burst frequency were adopted as representative characteristics for neuronal networks analysis. Functional connectivity was estimated by means of cross-covariance analysis and graph theory. The results demonstrated that the functional connectivity of the in vitro neuronal networks formed in the microchannel has been apparently reinforced, corresponding to improve neuronal network density and increased small-worldness.

Molecular basis for the specific recognition of the metazoan cyclic GMP-AMP by the innate immune adaptor protein STING.

Cyclic GMP-AMP containing a unique combination of mixed phosphodiester linkages (2'3'-cGAMP) is an endogenous second messenger molecule that activates the type-I IFN pathway upon binding to the homodimer of the adaptor protein STING on the surface of endoplasmic reticulum membrane. However, the preferential binding of the asymmetric ligand 2'3'-cGAMP to the symmetric dimer of STING represents a physicochemical enigma. Here we show that 2'3'-cGAMP, but not its linkage isomers, adopts an organized free-ligand conformation that resembles the STING-bound conformation and pays low entropy and enthalpy costs in converting into the active conformation. Our results demonstrate that analyses of free-ligand conformations can be as important as analyses of protein conformations in understanding protein-ligand interactions.

Sensitive and Precise Characterization of Combinatorial Histone Modifications by Selective Derivatization Coupled with RPLC-EThcD-MS/MS.

Deciphering the combinatorial histone codes has been a long-standing interest in the epigenetics field, which requires the reliable and robust characterization of the post-translational modifications (PTMs) coexisting on histones. To this end, weak cation exchange hydrophilic interaction liquid chromatography is commonly used in middle-down liquid chromatography-mass spectrometry approaches for online separation of variously modified histone peptides. Here we provide a novel strategy that combines the selective histone peptide derivatization using N-hydroxysuccinimide propionate ester with reversed-phase liquid chromatography (RPLC) for the robust, sensitive, and reliable characterization of combinatorial histone PTMs. Derivatization amplifies the subtle physical differences between similarly modified histone peptides, thereby allowing baseline separation of these peptides by standard RPLC. Also, the sensitivity of MS is enhanced greatly by derivatization due to the increased peptide hydrophobicity and concentrated charge-state envelope during electrospray ionization. Furthermore, we systematically optimized the dual electron transfer and higher energy collision dissociation and achieved near-complete peptide sequence coverage in MS/MS spectra, allowing highly precise and reliable PTM identification. Using this method, we identified 311 and 293 combinations of histone H3 PTMs from the lymphoma cells Karpas-422 with/without drug treatment, confirming the advantages of our method in serving as a platform for profiling combinatorial histone PTMs.

Low-fidelity alternative DNA repair carcinogenesis theory may interpret many cancer features and anticancer strategies.

We have proposed that the low-fidelity compensatory backup alternative DNA repair pathways drive multistep carcinogenesis. Here, we apply it to interpret the clinical features of cancer, such as mutator phenotype, tissue specificity, age specificity, diverse types of cancers originated from the same type of tissue, cancer susceptibility of patients with DNA repair-defective syndromes, development of cancer only for a selected number of individuals among those that share the same genetic defect, invasion and metastasis. Clinically, the theory predicts that to improve the efficacy of molecular targeted or synthetic lethal therapy, it may be crucial to inhibit the low-fidelity compensatory alternative DNA repair either directly or by blocking the signal transducers of the sustained microenvironmental stress.

HDAC6 mutations rescue human tau-induced microtubule defects in Drosophila.

Neurons from the brains of Alzheimer's disease (AD) and related tauopathy patients contain neurofibrillary tangles composed of hyperphosphorylated tau protein. Tau normally stabilizes microtubules (MTs); however, tau hyperphosphorylation leads to loss of this function with consequent MT destabilization and neuronal dysfunction. Accordingly, MT-stabilizing drugs such as paclitaxel and epothilone D have been shown as possible therapies for AD and related tauopathies. However, MT-stabilizing drugs have common side effects such as neuropathy and neutropenia. To find previously undescribed suppressors of tau-induced MT defects, we established a Drosophila model ectopically expressing human tau in muscle cells, which allow for clear visualization of the MT network. Overexpressed tau was hyperphosphorylated and resulted in decreased MT density and greater fragmentation, consistent with previous reports in AD patients and mouse models. From a genetic screen, we found that a histone deacetylase 6 (HDAC6) null mutation rescued tau-induced MT defects in both muscles and neurons. Genetic and pharmacological inhibition of the tubulin-specific deacetylase activity of HDAC6 indicates that the rescue effect may be mediated by increased MT acetylation. These findings reveal HDAC6 as a unique potential drug target for AD and related tauopathies.

Low-fidelity compensatory backup alternative DNA repair pathways may unify current carcinogenesis theories.

The somatic mutation carcinogenesis theory has dominated for decades. The alternative theory, tissue organization field theory, argues that the development of cancer is determined by the surrounding microenvironment. However, neither theory can explain all features of cancer. As cancers share the features of uncontrolled proliferation and genomic instability, they are likely to have the same pathogenesis. It has been found that various DNA repair pathways within a cell crosstalk with one another, forming a DNA repair network. When one DNA repair pathways is defective, the others may work as compensatory backups. The latter pathways are explored for synthetic lethal anticancer therapy. In this article, we extend the concept of compensatory alternative DNA repair to unify the theories. We propose that the microenvironmental stress can activate low-fidelity compensatory alternative DNA repair, causing mutations. If the mutation occurs to a DNA repair gene, this secondarily mutated gene can lead to even more mutated genes, including those related to other DNA repair pathways, eventually destabilizing the genome. Therefore, the low-fidelity compensatory alternative DNA repair may mediate microenvironment-dependent carcinogenesis. The proposal seems consistent with the view of evolution: the environmental stress causes mutations to adapt to the changing environment.