Microbiome dynamics in immune checkpoint blockade.

Immune checkpoint blockade (ICB) is one of the leading immunotherapies, although a variable extent of resistance has been observed among patients and across cancer types. Among the efforts underway to overcome this challenge, the microbiome has emerged as a factor affecting the responsiveness and efficacy of ICB. Active research, facilitated by advances in sequencing techniques, is assessing the predominant influence of the intestinal microbiome, as well as the effects of the presence of an intratumoral microbiome. In this review, we describe recent findings from clinical trials, observational studies of human patients, and animal studies on the impact of the microbiome on the efficacy of ICB, highlighting the role of the intestinal and tumor microbiomes and the contribution of methodological advances in their study.

Deep Learning-Based Prediction Model for Gait Recovery after a Spinal Cord Injury.

Predicting gait recovery after a spinal cord injury (SCI) during an acute rehabilitation phase is important for planning rehabilitation strategies. However, few studies have been conducted on this topic to date. In this study, we developed a deep learning-based prediction model for gait recovery after SCI upon discharge from an acute rehabilitation facility. Data were collected from 405 patients with acute SCI admitted to the acute rehabilitation facility of Korea University Anam Hospital between June 2008 and December 2022. The dependent variable was Functional Ambulation Category at the time of discharge (FAC-DC). Seventy-one independent variables were selected from the existing literature: basic information, International Standards for Neurological Classification of SCI scores, neurogenic bladders, initial FAC, and somatosensory-evoked potentials of the lower extremity. Recurrent neural network (RNN), linear regression (LR), Ridge, and Lasso methods were compared for FAC-DC prediction in terms of the root-mean-squared error (RMSE). RNN variable importance, which is the RMSE gap between a complete RNN model and an RNN model excluding a certain variable, was used to evaluate the contribution of this variable. Based on the results of this study, the performance of the RNN was far better than that of LR, Ridge, and Lasso. The respective RMSEs were 0.3738, 2.2831, 1.3161, and 1.0246 for all the participants; 0.3727, 1.7176, 1.3914, and 1.3524 for those with trauma; and 0.3728, 1.7516, 1.1012, and 0.8889 for those without trauma. In terms of RNN variable importance, lower-extremity motor strength (right and left ankle dorsiflexors, right knee extensors, and left long toe extensors) and the neurological level of injury were ranked among the top five across the boards. Therefore, initial FAC was the seventh, third, and ninth most important predictor for all participants, those with trauma, and those without trauma, respectively. In conclusion, this study developed a deep learning-based prediction model with excellent performance for gait recovery after SCI at the time of discharge from an acute rehabilitation facility. This study also demonstrated the strength of deep learning as an explainable artificial intelligence method for identifying the most important predictors.

Photosynthetic responses of large old Zelkova serrata (Thunb.) Makino trees to different growth environments.

Large old trees, which provide ecosystem services and serve as a historical and cultural heritage, are exposed to various environmental threats, such as habitat fragmentation and climate change, necessitating diagnosis of tangible and intangible stresses and their effects on tree growth for effective management. This study investigated the photosynthetic characteristics of 25 large old Zelkova serrata (Thunb.) Makino trees in Chungcheong Province, Korea, and identified the physical environmental factors affecting their physiological responses. Maximum assimilation rate (Amax) was the highest in July (summer), transpiration rate (E) and stomatal conductance (gs) increased from May (spring) to September (fall), and water use efficiency (WUE) was the highest in May (spring) and decreased until September (fall). Amax decreased as tree height increased. Ambient CO2 and vapor pressure deficit (VPD) were negatively correlated with photosynthetic parameters throughout the growth season and in July (summer) and September (fall), respectively. Physical environmental factors exhibited complex effect on physiological activities, which increased with wide growth space and decreased with deep soil covering and high impervious ground surface ratio. Physiological responses differed with surface types within the growth space, with bare land showing higher mean Amax, E, and gs than areas with mulching material or concrete. This study quantitatively determined the physiological activities of large old Z. serrata and proposes appropriate management measures for ensuring their healthy growth in abiotic stress environment.

A densely packed air-stable free-standing film with FeP nanoparticles@C@P-doped reduced graphene oxide for sodium-ion batteries.

Developing a facile strategy which enhances the structural stability and air/moisture stability of transition metal phosphides for practical applications is important but challenging. Herein, we designed a densely packed free-standing film consisting of carbon-coated FeP nanoparticles anchored on P-doped graphene (FeP@C@PG film) through solventless thermal decomposition and the roll-press method. Phytic acid serves a multifunctional role as both a phosphorus source to prepare ultrafine FeP nanoparticles and a protective layer to improve air stability along with hydrophobic graphene and maximize the utilization of phosphide. This structure can enhance electron/ion transport kinetics, allowing for full utilization of active materials, and buffer large volume expansions while preventing pulverization/aggregation during cycling. Noticeably, the densely packed structure can greatly enhance oxidation resistance by effectively blocking the penetration of air/moisture. Therefore, the FeP@C@PG film delivers a stable reversible capacity of 536.6 mA h g-1 after 1000 cycles at 1 A g-1 with good capacity retention, an excellent rate capability of 440.7 mA h g-1 at 5 A g-1, and excellent oxidation stability at 80 °C in air. Furthermore, a pouch-type full-cell exhibits excellent rate/cycling performance and bendability. This study provides a new direction for the rational design and practical applications of advanced P-based materials used in alkali metal-ion batteries.

Chemical constituents of the culture broth of Dentipellis fragilis and their anti-inflammatory activities.

Seven undescribed compounds, dentipellinones A‒D (1, 2, 5, and 6), dentipellinol (3), methoxyerinaceolactone B (4), and erinaceolactomer A (7), were isolated from the culture broth of Dentipellis fragilis. Chemical structures of these isolated compounds were determined by analyses of 1D and 2D-NMR and MS data in comparison with data reported in the literature. Absolute configurations of 1‒7 were also determined by Electronic Circular Dichroism calculations. The isolated compounds were evaluated for their anti-inflammatory effects on NO production and pro-inflammatory cytokines levels in LPS-stimulated RAW264.7 cells. Compounds 5 and 7 were evaluated for their anti-inflammatory effects on NO production and pro-inflammatory cytokine levels in LPS-stimulated RAW264.7 cells. They exhibited inhibitory effects on LPS-induced NO production in a dose-dependent manner, and significantly reduced the levels of inflammatory-related cytokines such as IL-1ß and IL-6. TNF-α was not involved in the anti-inflammatory effects of these compounds. Finally, compounds 5 and 7 showed significant anti-inflammatory effects.

Explainable artificial intelligence on life satisfaction, diabetes mellitus and its comorbid condition.

This study uses artificial intelligence for testing (1) whether the comorbidity of diabetes and its comorbid condition is very strong in the middle-aged or old (hypothesis 1) and (2) whether major determinants of the comorbidity are similar for different pairs of diabetes and its comorbid condition (hypothesis 2). Three pairs are considered, diabetes-cancer, diabetes-heart disease and diabetes-mental disease. Data came from the Korean Longitudinal Study of Ageing (2016-2018), with 5527 participants aged 56 or more. The evaluation of the hypotheses were based on (1) whether diabetes and its comorbid condition in 2016 were top-5 determinants of the comorbidity in 2018 (hypothesis 1) and (2) whether top-10 determinants of the comorbidity in 2018 were similar for different pairs of diabetes and its comorbid condition (hypothesis 2). Based on random forest variable importance, diabetes and its comorbid condition in 2016 were top-2 determinants of the comorbidity in 2018. Top-10 determinants of the comorbidity in 2018 were the same for different pairs of diabetes and its comorbid condition: body mass index, income, age, life satisfaction-health, life satisfaction-economic, life satisfaction-overall, subjective health and children alive in 2016. In terms of SHAP values, the probability of the comorbidity is expected to decrease by 0.02-0.03 in case life satisfaction overall is included to the model. This study supports the two hypotheses, highlighting the importance of preventive measures for body mass index, socioeconomic status, life satisfaction and family support to manage diabetes and its comorbid condition.

Regulation of c-SMAC formation and AKT-mTOR signaling by the TSG101-IFT20 axis in CD4+ T cells.

CD4+ T cells play major roles in the adaptive immune system, which requires antigen recognition, costimulation, and cytokines for its elaborate orchestration. Recent studies have provided new insight into the importance of the supramolecular activation cluster (SMAC), which comprises concentric circles and is involved in the amplification of CD4+ T cell activation. However, the underlying mechanism of SMAC formation remains poorly understood. Here, we performed single-cell RNA sequencing of CD4+ T cells left unstimulated and stimulated with anti-CD3 and anti-CD28 antibodies to identify novel proteins involved in their regulation. We found that intraflagellar transport 20 (IFT20), previously known as cilia-forming protein, was upregulated in antibody-stimulated CD4+ T cells compared to unstimulated CD4+ T cells. We also found that IFT20 interacted with tumor susceptibility gene 101 (TSG101), a protein that endocytoses ubiquitinated T-cell receptors. The interaction between IFT20 and TSG101 promoted SMAC formation, which led to amplification of AKT-mTOR signaling. However, IFT20-deficient CD4+ T cells showed SMAC malformation, resulting in reduced CD4+ T cell proliferation, aerobic glycolysis, and cellular respiration. Finally, mice with T-cell-specific IFT20 deficiency exhibited reduced allergen-induced airway inflammation. Thus, our data suggest that the IFT20-TSG101 axis regulates AKT-mTOR signaling via SMAC formation.

ERdj5 protects goblet cells from endoplasmic reticulum stress-mediated apoptosis under inflammatory conditions.

Endoplasmic reticulum stress is closely associated with the onset and progression of inflammatory bowel disease. ERdj5 is an endoplasmic reticulum-resident protein disulfide reductase that mediates the cleavage and degradation of misfolded proteins. Although ERdj5 expression is significantly higher in the colonic tissues of patients with inflammatory bowel disease than in healthy controls, its role in inflammatory bowel disease has not yet been reported. In the current study, we used ERdj5-knockout mice to investigate the potential roles of ERdj5 in inflammatory bowel disease. ERdj5 deficiency causes severe inflammation in mouse colitis models and weakens gut barrier function by increasing NF-κB-mediated inflammation. ERdj5 may not be indispensable for goblet cell function under steady-state conditions, but its deficiency induces goblet cell apoptosis under inflammatory conditions. Treatment of ERdj5-knockout mice with the chemical chaperone ursodeoxycholic acid ameliorated severe colitis by reducing endoplasmic reticulum stress. These findings highlight the important role of ERdj5 in preserving goblet cell viability and function by resolving endoplasmic reticulum stress.

Blood monocyte-derived CD169+ macrophages contribute to antitumor immunity against glioblastoma.

Infiltrating tumor-associated macrophages (TAM) are known to impede immunotherapy against glioblastoma (GBM), however, TAMs are heterogeneous, and there are no clear markers to distinguish immunosuppressive and potentially immune-activating populations. Here we identify a subset of CD169+ macrophages promoting an anti-tumoral microenvironment in GBM. Using single-cell transcriptome analysis, we find that CD169+ macrophages in human and mouse gliomas produce pro-inflammatory chemokines, leading to the accumulation of T cells and NK cells. CD169 expression on macrophages facilitates phagocytosis of apoptotic glioma cells and hence tumor-specific T cell responses. Depletion of CD169+ macrophages leads to functionally impaired antitumor lymphocytes and poorer survival of glioma-bearing mice. We show that NK-cell-derived IFN-γ is critical for the accumulation of blood monocyte-derived CD169+ macrophages in gliomas. Our work thus identifies a well-distinguished TAM subset promoting antitumor immunity against GBM, and identifies key factors that might shift the balance from immunosuppressive to anti-tumor TAM.

Protocol to analyze antitumor immunity of orthotopic injection and spontaneous murine high-grade glioma models using flow cytometry and single-cell RNA sequencing.

Despite the recognized importance of antitumor immunity, our understanding of brain tumor immunity is poor. Orthotopic injection models have been widely used for immunological analyses. However, these models have limitations in analysis of antitumor immunity because the approach involves drilling skulls and injecting tumor cells, which can induce adverse effects. We describe a protocol for the induction of spontaneous brain tumor model, isolation of single cells from brain tumor microenvironment, and analysis of the immune responses using scRNA-seq and flow cytometry. For complete details on the use and execution of this protocol, please refer to Park et al. (2021).

Gram-negative bacteria and their lipopolysaccharides in Alzheimer's disease: pathologic roles and therapeutic implications.

Alzheimer's disease (AD) is the most serious age-related neurodegenerative disease and causes destructive and irreversible cognitive decline. Failures in the development of therapeutics targeting amyloid-ß (Aß) and tau, principal proteins inducing pathology in AD, suggest a paradigm shift towards the development of new therapeutic targets. The gram-negative bacteria and lipopolysaccharides (LPS) are attractive new targets for AD treatment. Surprisingly, an altered distribution of gram-negative bacteria and their LPS has been reported in AD patients. Moreover, gram-negative bacteria and their LPS have been shown to affect a variety of AD-related pathologies, such as Aß homeostasis, tau pathology, neuroinflammation, and neurodegeneration. Moreover, therapeutic approaches targeting gram-negative bacteria or gram-negative bacterial molecules have significantly alleviated AD-related pathology and cognitive dysfunction. Despite multiple evidence showing that the gram-negative bacteria and their LPS play a crucial role in AD pathogenesis, the pathogenic mechanisms of gram-negative bacteria and their LPS have not been clarified. Here, we summarize the roles and pathomechanisms of gram-negative bacteria and LPS in AD. Furthermore, we discuss the possibility of using gram-negative bacteria and gram-negative bacterial molecules as novel therapeutic targets and new pathological characteristics for AD.

Monocytes Contribute to IFN-ß Production via the MyD88-Dependent Pathway and Cytotoxic T-Cell Responses against Mucosal Respiratory Syncytial Virus Infection.

Respiratory syncytial virus (RSV) is the leading cause of respiratory viral infection in infants and children. However, little is known about the contribution of monocytes to antiviral responses against RSV infection. We identified the IFN-ß production of monocytes using IFN-ß/YFP reporter mice. The kinetic analysis of IFN-ß-producing cells in in vivo RSV-infected lung cells indicated that monocytes are recruited to the inflamed lung during the early phase of infection. These cells produced IFN-ß via the myeloid differentiation factor 88-mediated pathway, rather than the TLR7- or mitochondrial antiviral signaling protein-mediated pathway. In addition, monocyte-ablated mice exhibited decreased numbers of IFN-γ-producing and RSV Ag-specific CD8+ T cells. Collectively, these data indicate that monocytes play pivotal roles in cytotoxic T-cell responses and act as type I IFN producers during RSV infection.

Recent Development of Flexible and Stretchable Supercapacitors Using Transition Metal Compounds as Electrode Materials.

Flexible and stretchable supercapacitors (FS-SCs) are promising energy storage devices for wearable electronics due to their versatile flexibility/stretchability, long cycle life, high power density, and safety. Transition metal compounds (TMCs) can deliver a high capacitance and energy density when applied as pseudocapacitive or battery-like electrode materials owing to their large theoretical capacitance and faradaic charge-storage mechanism. The recent development of TMCs (metal oxides/hydroxides, phosphides, sulfides, nitrides, and selenides) as electrode materials for FS-SCs are discussed here. First, fundamental energy-storage mechanisms of distinct TMCs, various flexible and stretchable substrates, and electrolytes for FS-SCs are presented. Then, the electrochemical performance and features of TMC-based electrodes for FS-SCs are categorically analyzed. The gravimetric, areal, and volumetric energy density of SC using TMC electrodes are summarized in Ragone plots. More importantly, several recent design strategies for achieving high-performance TMC-based electrodes are highlighted, including material composition, current collector design, nanostructure design, doping/intercalation, defect engineering, phase control, valence tuning, and surface coating. Integrated systems that combine wearable electronics with FS-SCs are introduced. Finally, a summary and outlook on TMCs as electrodes for FS-SCs are provided.

Pharmacophore-Based Virtual Screening of Novel Competitive Inhibitors of the Neurodegenerative Disease Target Kynurenine-3-Monooxygenase.

The pathogenesis of several neurodegenerative diseases such as Alzheimer's or Huntington's disease has been associated with metabolic dysfunctions caused by imbalances in the brain and cerebral spinal fluid levels of neuroactive metabolites. Kynurenine monooxygenase (KMO) is considered an ideal therapeutic target for the regulation of neuroactive tryptophan metabolites. Despite significant efforts, the known KMO inhibitors lack blood-brain barrier (BBB) permeability and upon the mimicking of the substrate binding mode, are subject to produce reactive oxygen species as a side reaction. The computational drug design is further complicated by the absence of complete crystal structure information for human KMO (hKMO). In the current work, we performed virtual screening of readily available compounds using several protein-ligand complex pharmacophores. Each of the pharmacophores accounts for one of three distinct reported KMO protein-inhibitor binding conformations. As a result, six novel KMO inhibitors were discovered based on an in vitro fluorescence assay. Compounds VS1 and VS6 were predicted to be BBB permeable and avoid the hydrogen peroxide production dilemma, making them valuable, novel hit compounds for further drug property optimization and advancement in the drug design pipeline.

Single Cell Transcriptomic Re-analysis of Immune Cells in Bronchoalveolar Lavage Fluids Reveals the Correlation of B Cell Characteristics and Disease Severity of Patients with SARS-CoV-2 Infection.

The coronavirus disease 2019 (COVID-19) pandemic (severe acute respiratory syndrome coronavirus 2) is a global infectious disease with rapid spread. Some patients have severe symptoms and clinical signs caused by an excessive inflammatory response, which increases the risk of mortality. In this study, we reanalyzed scRNA-seq data of cells from bronchoalveolar lavage fluids of patients with COVID-19 with mild and severe symptoms, focusing on Ab-producing cells. In patients with severe disease, B cells seemed to be more activated and expressed more immunoglobulin genes compared with cells from patients with mild disease, and macrophages expressed higher levels of the TNF superfamily member B-cell activating factor but not of APRIL (a proliferation-inducing ligand). In addition, macrophages from patients with severe disease had increased pro-inflammatory features and pathways associated with Fc receptor-mediated signaling, compared with patients with mild disease. CCR2-positive plasma cells accumulated in patients with severe disease, probably because of increased CCL2 expression on macrophages from patients with severe disease. Together, these results support the hypothesis that different characteristics of B cells might be associated with the severity of COVID-19 infection.

Tumor hypoxia represses γδ T cell-mediated antitumor immunity against brain tumors.

The anatomic location and immunologic characteristics of brain tumors result in strong lymphocyte suppression. Consequently, conventional immunotherapies targeting CD8 T cells are ineffective against brain tumors. Tumor cells escape immunosurveillance by various mechanisms and tumor cell metabolism can affect the metabolic states and functions of tumor-infiltrating lymphocytes. Here, we discovered that brain tumor cells had a particularly high demand for oxygen, which affected γδ T cell-mediated antitumor immune responses but not those of conventional T cells. Specifically, tumor hypoxia activated the γδ T cell protein kinase A pathway at a transcriptional level, resulting in repression of the activatory receptor NKG2D. Alleviating tumor hypoxia reinvigorated NKG2D expression and the antitumor function of γδ T cells. These results reveal a hypoxia-mediated mechanism through which brain tumors and γδ T cells interact and emphasize the importance of γδ T cells for antitumor immunity against brain tumors.

The role of dendritic cells in tumor microenvironments and their uses as therapeutic targets.

Dendritic cells (DC), which consist of several different subsets, specialize in antigen presentation and are critical for mediating the innate and adaptive immune responses. DC subsets can be classified into conventional, plasmacytoid, and monocyte-derived DC in the tumor microenvironment, and each subset plays a different role. Because of the role of intratumoral DCs in initiating antitumor immune responses with tumor-derived antigen presentation to T cells, DCs have been targeted in the treatment of cancer. By regulating the functionality of DCs, several DCbased immunotherapies have been developed, including administration of tumor-derived antigens and DC vaccines. In addition, DCs participate in the mechanisms of classical cancer therapies, such as radiation therapy and chemotherapy. Thus, regulating DCs is also important in improving current cancer therapies. Here, we will discuss the role of each DC subset in antitumor immune responses, and the current status of DC-related cancer therapies. [BMB Reports 2021; 54(1): 31-43].

Multivalent DNA vaccine protects against genital herpes by T-cell immune induction in vaginal mucosa.

Genital herpes is one of the most common sexually transmitted infections (STIs), and it is mainly caused by the neurotropic herpes simplex virus (HSV-2). Not only does this infection cause ulcers, but HSV-2 can also stay in a latent state in the nervous system of the host throughout their lifespan. As a result, many people do not know that they harbor this infection. Moreover, HSV-2 serves as a major risk factor for human immunodeficiency virus (HIV) infection and can be transmitted to the fetus. Despite the high risk of infection and adverse effects, attempts at development of an effective vaccine for HSV-2 have not yet been successful. In this study, we developed a DNA vaccine for HSV-2 (SL-V20). This multivalent DNA vaccine effectively reduced the pathological symptoms of infection and induced efficient elimination of the virus in a mouse model. Intramuscular injection of SL-V20 led to induction of an HSV-2-specific T-cell response in the vagina, the major infection site, and in draining lymph organs. Dendritic cells (DCs), especially basic leucine zipper ATF-like transcription factor 3 (Baft3)+ DCs and partially interferon regulatory factor 4 (Irf4)+ DCs, were involved in this T-cell-mediated protective response, while B cells were dispensable for these prophylactic effects. This study demonstrates that SL-V20 offers a novel and effective vaccine against vaginal HSV-2 infection and may be applicable to patients, pending validation in clinical studies.

Exogenous Interleukin-33 Contributes to Protective Immunity via Cytotoxic T-Cell Priming against Mucosal Influenza Viral Infection.

Influenza is an infectious respiratory illness caused by the influenza virus. Though vaccines against influenza exist, they have limited efficacy. To additionally develop effective treatments, there is a need to study the mechanisms of host defenses from influenza viral infections. To date, the mechanism by which interleukin (IL)-33 modulates the antiviral immune response post-influenza infection is unclear. In this study, we demonstrate that exogenous IL-33 enhanced antiviral protection against influenza virus infection. Exogenous IL-33 induced the recruitment of dendritic cells, increased the secretion of pro-inflammatory cytokine IL-12, and promoted cytotoxic T-cell responses in the local microenvironment. Thus, our findings suggest a role of exogenous IL-33 in the antiviral immune response against influenza infection.

Interactions between Host Immunity and Skin-Colonizing Staphylococci: No Two Siblings Are Alike.

As the outermost layer of the body, the skin harbors innumerable and varied microorganisms. These microorganisms interact with the host, and these interactions contribute to host immunity. One of the most abundant genera of skin commensals is Staphylococcus. Bacteria belonging to this genus are some of the most influential commensals that reside on the skin. For example, colonization by Staphylococcus aureus, a well-known pathogen, increases inflammatory responses within the skin. Conversely, colonization by Staphylococcus epidermis, a coagulase-negative staphylococcal species that are prevalent throughout the skin, can be innocuous or beneficial. Thus, manipulating the abundance of these two bacterial species likely alters the skin microbiome and modulates the cutaneous immune response, with potential implications for various inflammation-associated skin diseases. Importantly, before researchers can begin manipulating the skin microbiome to prevent and treat disease, they must first fully understand how these two species can modulate the cutaneous immune response. In this review, we discuss the nature of the interactions between these two bacterial species and immune cells within the skin, discussing their immunogenicity within the context of skin disorders.