Single-Cell Informatics for Tumor Microenvironment and Immunotherapy.

Cancer comprises malignant cells surrounded by the tumor microenvironment (TME), a dynamic ecosystem composed of heterogeneous cell populations that exert unique influences on tumor development. The immune community within the TME plays a substantial role in tumorigenesis and tumor evolution. The innate and adaptive immune cells "talk" to the tumor through ligand-receptor interactions and signaling molecules, forming a complex communication network to influence the cellular and molecular basis of cancer. Such intricate intratumoral immune composition and interactions foster the application of immunotherapies, which empower the immune system against cancer to elicit durable long-term responses in cancer patients. Single-cell technologies have allowed for the dissection and characterization of the TME to an unprecedented level, while recent advancements in bioinformatics tools have expanded the horizon and depth of high-dimensional single-cell data analysis. This review will unravel the intertwined networks between malignancy and immunity, explore the utilization of computational tools for a deeper understanding of tumor-immune communications, and discuss the application of these approaches to aid in diagnosis or treatment decision making in the clinical setting, as well as the current challenges faced by the researchers with their potential future improvements.

miR-125b reverses cisplatin resistance by regulating autophagy via targeting RORA/BNIP3L axis in lung adenocarcinoma.

The platinum-based chemotherapy is one of the most frequently used treatment protocols for lung adenocarcinoma (LUAD), and chemoresistance, however, usually results in treatment failure and limits its application in the clinic. It has been shown that microRNAs (miRNAs) play a significant role in tumor chemoresistance. In this study, miR-125b was identified as a specific cisplatin (DDP)-resistant gene in LUAD, as indicated by the bioinformatics analysis and the real-time quantitative PCR assay. The decreased serum level of miR-125b in LUAD patients was correlated with the poor treatment response rate and short survival time. MiR-125b decreased the A549/DDP proliferation, and the multiple drug resistance- and autophagy-related protein expression levels, which were all reversed by the inhibition of miR-125b. In addition, xenografts of human tumors in nude mice were suppressed by miR-125b, demonstrating that through autophagy regulation, miR-125b could reverse the DDP resistance in LUAD cells, both in vitro and in vivo. Further mechanistic studies indicated that miR-125b directly repressed the expression levels of RORA and its downstream BNIP3L, which in turn inhibited autophagy and reversed chemoresistance. Based on these findings, miR-125b in combination with DDP might be an effective treatment option to overcome DDP resistance in LUAD.

Stroma-infiltrating T cell spatiotypes define immunotherapy outcomes in adolescent and young adult patients with melanoma.

The biological underpinnings of therapeutic resistance to immune checkpoint inhibitors (ICI) in adolescent and young adult (AYA) melanoma patients are incompletely understood. Here, we characterize the immunogenomic profile and spatial architecture of the tumor microenvironment (TME) in AYA (aged ≤ 30 years) and older adult (aged 31-84 years) patients with melanoma, to determine the AYA-specific features associated with ICI treatment outcomes. We identify two ICI-resistant spatiotypes in AYA patients with melanoma showing stroma-infiltrating lymphocytes (SILs) that are distinct from the adult TME. The SILhigh subtype was enriched in regulatory T cells in the peritumoral space and showed upregulated expression of immune checkpoint molecules, while the SILlow subtype showed a lack of immune activation. We establish a young immunosuppressive melanoma score that can predict ICI responsiveness in AYA patients and propose personalized therapeutic strategies for the ICI-resistant subgroups. These findings highlight the distinct immunogenomic profile of AYA patients, and individualized TME features in ICI-resistant AYA melanoma that require patient-specific treatment strategies.

Genomic insights into the clonal reproductive Opuntia cochenillifera: mitochondrial and chloroplast genomes of the cochineal cactus for enhanced understanding of structural dynamics and evolutionary implications.

Background: The cochineal cactus (Opuntia cochenillifera), notable for its substantial agricultural and industrial applications, predominantly undergoes clonal reproduction, which presents significant challenges in breeding and germplasm innovation. Recent developments in mitochondrial genome engineering offer promising avenues for introducing heritable mutations, potentially facilitating selective sexual reproduction through the creation of cytoplasmic male sterile genotypes. However, the lack of comprehensive mitochondrial genome information for Opuntia species hinders these efforts. Here, we intended to sequence and characterize its mitochondrial genome to maximize the potential of its genomes for evolutionary studies, molecular breeding, and molecular marker developments. Results: We sequenced the total DNA of the O. cochenillifera using DNBSEQ and Nanopore platforms. The mitochondrial genome was then assembled using a hybrid assembly strategy using Unicycler software. We found that the mitochondrial genome of O. cochenillifera has a length of 1,156,235 bp, a GC content of 43.06%, and contains 54 unique protein-coding genes and 346 simple repeats. Comparative genomic analysis revealed 48 homologous fragments shared between mitochondrial and chloroplast genomes, with a total length of 47,935 bp. Additionally, the comparison of mitochondrial genomes from four Cactaceae species highlighted their dynamic nature and frequent mitogenomic reorganizations. Conclusion: Our study provides a new perspective on the evolution of the organelle genome and its potential application in genetic breeding. These findings offer valuable insights into the mitochondrial genetics of Cactaceae, potentially facilitating future research and breeding programs aimed at enhancing the genetic diversity and adaptability of O. cochenillifera by leveraging its unique mitochondrial genome characteristics.

Artesunate inhibits macrophage-like phenotype switching of vascular smooth muscle cells and attenuates vascular inflammatory injury in atherosclerosis via NLRP3.

Inflammation is one of the main pathogenic factors of atherosclerosis (AS), and the phenotypic transformation of macrophages in human vascular smooth muscle cells (HVSMCs) contributes to the inflammatory injury of blood vessels and the formation of atherosclerotic plaques. Artesunate reportedly exerts anti-inflammatory activity against AS. Herein, we aimed to explore the artesunate-mediated anti-inflammatory and HVSMC phenotypic switch effects against AS and elucidate potential underlying mechanisms. In vitro, artesunate decreased expression of NLRP3, caspase-1, and interleukin (IL)- 1ß. Artesunate significantly inhibited low-density lipoprotein (LDL) expression in HVSMCs and macrophages. In vivo, artesunate reduced atherosclerotic plaque formation in high-fat diet (HFD)-fed ApoE-/- mice, as well as decreased NLRP3 and CD68 expression in atherosclerotic plaques. Artesunate decreased serum levels of triglycerides and increased high-density lipoprotein levels in HFD-med mice; however, serum levels of total cholesterol and LDL were unaltered. Treatment with artesunate substantially increased α-smooth muscle actin expression in aortic tissues while inhibiting expression levels of NLRP3, IL-1ß, heparinase, matrix metalloproteinase 9, and Krüppel-like factor 4 (KLF4). Collectively, our findings suggest that artesunate-mediated effects may involve inhibition of the ERK1/2/NF-κB/IL-1ß pathway in HVSMCs via the downregulation of NLRP3 expression. Thus, artesunate could serve as a novel strategy to treat AS by inhibiting AS plaque formation and suppressing macrophage-like phenotype switching of HVSMCs.

Ailanthone induces autophagy and ferroptosis in non­small cell lung cancer Lewis cells.

Ailanthone (AIL), a monomer derived from ailanthus in Chinese medicine, has been demonstrated to have antitumor effects, albeit the underlying mechanism is unknown. Autophagy and ferroptosis are two modes of cell death that have been championed as potential mechanisms implicated in the antitumor effects of various drugs. The present study demonstrated that AIL effectively suppresses the Lewis cell proliferation in non-small cell lung cancer using MTT and colony formation assays. Autophagy and ferroptosis were verified using western blotting, immunofluorescence and ferroptosis detection. Additionally, the findings revealed that regulating the AMPK/mTOR/p70S6k signaling pathway may be the underlying mechanism for the antitumor effect of AIL. The present study established a theoretical foundation for further research into the utilization of AIL as a novel antitumor approach.

Identification of cuproptosis-related molecular classification and characteristic genes in ulcerative colitis.

Ulcerative colitis (UC) is a refractory inflammatory disease with imbalances in intestinal mucosal homeostasis. Cuproptosis serves as newly identified programmed cell death (PCD) form involved in UC. In the study, UC-related datasets were extracted from the Gene Expression Omnibus (GEO) database. A comparison of UC patients and healthy controls identified 11 differentially expressed cuproptosis-related genes (DE-CRGs), where FDX1, LIAS, and DLAT were differentially expressed in UC groups from the mouse models and clinical samples, with their expression correlating with disease severity. By comprehending weighted gene co-expression network analysis (WGCNA) and differential expression analysis, the key genes common to the module genes relevant to different cuproptosis-related clusters and differentially expressed genes (DEGs) both in different clusters and patients with and without UC were identified using several bioinformatic analysis. Furthermore, the mRNA levels of four characteristic genes with diagnostic potential demonstrated significant decrease in both mouse models and clinical UC samples. Our discoveries offer a theoretical foundation for cuproptosis effect in UC.

Assessing social cognition in patients with schizophrenia and healthy controls using the reading the mind in the eyes test (RMET): a systematic review and meta-regression.

The reading the mind in the eyes test (RMET) - which assesses the theory of mind component of social cognition - is often used to compare social cognition between patients with schizophrenia and healthy controls. There is, however, no systematic review integrating the results of these studies. We identified 198 studies published before July 2020 that administered RMET to patients with schizophrenia or healthy controls from three English-language and two Chinese-language databases. These studies included 41 separate samples of patients with schizophrenia (total n = 1836) and 197 separate samples of healthy controls (total n = 23 675). The pooled RMET score was 19.76 (95% CI 18.91-20.60) in patients and 25.53 (95% CI 25.19-25.87) in controls (z = 12.41, p < 0.001). After excluding small-sample outlier studies, this difference in RMET performance was greater in studies using non-English v. English versions of RMET (Chi [Q] = 8.54, p < 0.001). Meta-regression analyses found a negative association of age with RMET score and a positive association of years of schooling with RMET score in both patients and controls. A secondary meta-analysis using a spline construction of 180 healthy control samples identified a non-monotonic relationship between age and RMET score - RMET scores increased with age before 31 and decreased with age after 31. These results indicate that patients with schizophrenia have substantial deficits in theory of mind compared with healthy controls, supporting the construct validity of RMET as a measure of social cognition. The different results for English versus non-English versions of RMET and the non-monotonic relationship between age and RMET score highlight the importance of the language of administration of RMET and the possibility that the relationship of aging with theory of mind is different from the relationship of aging with other types of cognitive functioning.

Deciphering the Plastomic Code of Chinese Hog-Peanut (Amphicarpaea edgeworthii Benth., Leguminosae): Comparative Genomics and Evolutionary Insights within the Phaseoleae Tribe.

The classification and phylogenetic relationships within the Phaseoleae tribe (Leguminosae) have consistently posed challenges to botanists. This study addresses these taxonomic intricacies, with a specific focus on the Glycininae subtribe, by conducting a comprehensive analysis of the highly conserved plastome in Amphicarpaea edgeworthii Benth., a critical species within this subtribe. Through meticulous genomic sequencing, we identified a plastome size of 148,650 bp, composed of 128 genes, including 84 protein-coding genes, 36 tRNA genes, and 8 rRNA genes. Comparative genomic analysis across seven Glycininae species illuminated a universally conserved circular and quadripartite structure, with nine genes exhibiting notable nucleotide diversity, signifying a remarkable genomic variability. Phylogenetic reconstruction of 35 Phaseoleae species underscores the affinity of Amphicarpaea with Glycine, placing Apios as a sister lineage to all other Phaseoleae species, excluding Clitorinae and Diocleinae subtribes. Intriguingly, Apios, Butea, Erythrina, and Spatholobus, traditionally clumped together in the Erythrininae subtribe, display paraphyletic divergence, thereby contesting their taxonomic coherence. The pronounced structural differences in the quadripartite boundary genes among taxa with unresolved subtribal affiliations demand a reevaluation of Erythrininae's taxonomic classification, potentially refining the phylogenetic contours of the tribe.

Stochastic dynamical analysis for the complex infectious disease model driven by multisource noises.

This paper mainly studies the dynamical behavior of the infectious disease model affected by white noise and Lévy noise. First, a stochastic model of infectious disease with secondary vaccination affected by noises is established. Besides, the existence and uniqueness of the global positive solution for the stochastic model are proved based on stochastic differential equations and Lyapunov function, then the asymptotic behavior of the disease-free equilibrium point is studied. Moreover, the sufficient conditions for the extinction of the disease are obtained and the analysis showed that different noise intensity could affect the extinction of infectious disease on different degree. Finally, the theoretical results are verified by numerical simulation and some suggestions have been put forward on how to prevent the spread of diseases are presented.

A Practical Approach Toward Highly Reproducible and High-Quality Perovskite Films Based on an Aging Treatment.

Solution processing of hybrid perovskite semiconductors is a highly promising approach for the fabrication of cost-effective electronic and optoelectronic devices. However, challenges with this approach lie in overcoming the controllability of the perovskite film morphology and the reproducibility of device efficiencies. Here, a facile and practical aging treatment (AT) strategy is reported to modulate the perovskite crystal growth to produce sufficiently high-quality perovskite thin films with improved homogeneity and full-coverage morphology. The resulting AT-films exhibit fewer defects, faster charge carrier transfer/extraction, and suppressed non-radiative recombination compared with reference. The AT-devices achieve a noticeable improvement in the reproducibility, operational stability, and photovoltaic performance of devices, with the average efficiency increased by 16%. It also demonstrates the feasibility and scalability of AT strategy in optimizing the film morphology and device performance for other perovskite components including MAPbI3 , (MAPbBr3 )15 (FAPbI3 )85 , and Cs0.05 (MAPbBr3 )0.17 (FAPbI3 )0.83 . This method opens an effective avenue to improve the quality of perovskite films and photovoltaic devices in a scalable and reproducible manner.

WLJP-025p, a homogeneous Lonicera japonica polysaccharide, attenuates atopic dermatitis by regulating the MAPK/NFκB/AP-1 axis via Act1.

Atopic dermatitis (AD) is usually treated with steroids, but long-term use is not an effective cure because side effects and disease aggravation. Therefore, more effective and safer treatments are needed. Using dexamethasone as the positive control, the mechanism of action of water-extracted homogeneous honeysuckle Lonicera japonica polysaccharide (WLJP-025p) to alleviate AD was studied. Mice were administered 2,4-dinitrochlorobenzene in their bare back and right ear to mimic an AD model. The efficacy of WLJP-025p in AD was assessed by measuring right ear thickness and skin lesion scores, pathological observation (haematoxylin-eosin and toluidine blue staining), and serum IgE and IL-1ß concentrations. The expression of relevant genes and proteins in the serum and back skin was detected using RT-qPCR, ELISA, western blotting, and immunofluorescence. Molecular docking and dynamic simulation of WLJP-025p and Act1 were performed. WLJP-025p considerably alleviated skin hyperplasia and pathological abnormalities in AD mice and inhibited the expression of Act1, Nucleus-P65, Nucleus-AP-1, and MAPK-related proteins in skin tissues. WLJP-025p formed a stable conformation with Act1, inhibited splenic Th17 differentiation, IL-17 release, and upregulated the expression of related skin barrier proteins. In conclusion, WLJP-025p affects the inflammation regulation via the MAPK/NFκB/AP-1 axis by binding to Act1, promotes the recovery of epithelial barrier function, and alleviates AD in mice.

Advances in Extraction, Purification, and Analysis Techniques of the Main Components of Kudzu Root: A Comprehensive Review.

Kudzu root (Pueraria lobate (Willd.) Ohwi, KR) is an edible plant with rich nutritional and medicinal values. Over the past few decades, an ample variety of biological effects of Pueraria isoflavone have been evaluated. Evidence has shown that Pueraria isoflavone can play an active role in antioxidant, anti-inflammatory, anti-cancer, neuroprotection, and cardiovascular protection. Over 50 isoflavones in kudzu root have been identified, including puerarin, daidzein, daidzin, 3'-hydroxy puerarin, and genistein, each with unambiguous structures. However, the application of these isoflavones in the development of functional food and health food still depends on the extraction, purification and identification technology of Pueraria isoflavone. In recent years, many green and novel extraction, purification, and identification techniques have been developed for the preparation of Pueraria isoflavone. This review provides an updated overview of these techniques, specifically for isoflavones in KR since 2018, and also discusses and compares the advantages and disadvantages of these techniques in depth. The intention is to provide a research basis for the green and efficient extraction, purification, and identification of Pueraria isoflavone and offers investigators a valuable reference for future studies on the KR.

Backbone N-methylation of peptides: Advances in synthesis and applications in pharmaceutical drug development.

Peptide-based drugs have garnered considerable attention in recent years owing to their increasingly crucial role in the treatment of diverse diseases. However, the limited pharmacokinetic properties of peptides have hindered their full potential. One prominent strategy for enhancing the druggability of peptides is N-methylation, which involves the addition of a methyl group to the nitrogen atom of the peptide backbone. This modification significantly improves the stability, bioavailability, receptor binding affinity and selectivity of peptide drug candidates. In this review, we provide a comprehensive overview of the advancements in synthetic methods for N-methylated peptide synthesis, as well as the associated limitations. Moreover, we explore the versatile effects of N-methylation on various aspects of peptide properties. Furthermore, we emphasize the efforts dedicated to N-methylated peptide pharmaceuticals that have successfully obtained marketing approval.

Champion Device Architectures for Low-Cost and Stable Single-Junction Perovskite Solar Cells.

High power conversion efficiencies (PCE), low energy payback time (EPBT), and low manufacturing costs render perovskite solar cells (PSCs) competitive; however, a relatively low operational stability impedes their large-scale deployment. In addition, state-of-the-art PSCs are made of expensive materials, including the organic hole transport materials (HTMs) and the noble metals used as the charge collection electrode, which induce degradation in PSCs. Thus, developing inexpensive alternatives is crucial to fostering the transition from academic research to industrial development. Combining a carbon-based electrode with an inorganic HTM has shown the highest potential and should replace noble metals and organic HTMs. In this review, we illustrate the incorporation of a carbon layer as a back contact instead of noble metals and inorganic HTMs instead of organic ones as two cornerstones for achieving optimal stability and economic viability for PSCs. We discuss the primary considerations for the selection of the absorbing layer as well as the electron-transporting layer to be compatible with the champion designs and ultimate architecture for single-junction PSCs. More studies regarding the long-term stability are still required. Using the recommended device architecture presented in this work would pave the way toward constructing low-cost and stable PSCs.

Solution-Processable Cu3BiS3 Thin Films: Growth Process Insights and Increased Charge Generation Properties by Interface Modification.

Cu3BiS3 thin films are fabricated via spin coating of precursor solutions containing copper and bismuth xanthates onto planar glass substrates or mesoporous metal oxide scaffolds followed by annealing at 300 °C to convert the metal xanthates into copper bismuth sulfide. Detailed insights into the film formation are gained from time-resolved simultaneous small and wide angle X-ray scattering measurements. The Cu3BiS3 films show a high absorption coefficient and a band gap of 1.55 eV, which makes them attractive for application in photovoltaic devices. Transient absorption spectroscopic measurements reveal that charge generation yields in mesoporous TiO2/Cu3BiS3 heterojunctions can be significantly improved by the introduction of an In2S3 interlayer, and long-lived charge carriers (t50% of 10 µs) are found.

Aucubin improves chronic unpredictable mild stress-induced depressive behavior in mice via the GR/NF-κB/NLRP3 axis.

Eucommia ulmoides Oliv (EUO) is a traditional therapeutic drug that tonifies the liver and kidney and may improve depression. However, the mechanism of action of the main component, aucubin (AU), is unknown. To study the therapeutic effect of AU, we constructed a chronic unpredictable mild stress (CUMS) depression model in mice. Depression-like behaviors, pathological damage, hormonal changes, inflammation, intranuclear expression of glucocorticoidreceptor (GR), and hippocampal protein expression were assessed. Immunofluorescence staining of the hippocampus showed that CUMS decreased neuronal regeneration, and axons were observed to be reduced and broken. Intracellular GR expression decreased in the hippocampus and hypothalamus, and serum levels of stress hormones increased. Furthermore, molecular changes indicative of pyroptosis were observed. AU administration reversed these changes and significantly improved the depression-like behavior induced by CUMS. Our results suggested that AU improves depression by promoting the intranuclear expression of GR and inhibiting nuclear factor-kappa B-mediated inflammatory activation-driven cell pyroptosis.

Multi-functionalized Metallo-Supramolecular Spoked Wheels: Their Emission-Tunable Hierarchically Assembled System with Dye Molecules.

Supramolecular architectures with multiple emissive units are especially appealing due to their desired properties, such as artificial light harvesting and white-light emission. But fully achieving multi-wavelength photoluminescence in a single supramolecular architecture remains a challenge. In this paper, functionalized supramolecular architectures containing twelve metal centers and six pyrene moieties were nearly quantitatively synthesized by multi-component self-assembly and fully characterized by 1D and 2D nuclear magnetic resonance, dynamic light scattering, electrospray ionization mass spectrometry, traveling-wave ion mobility mass spectrometry, and transmission electron microscopy. Moreover, the hierarchical nano-assemblies were prepared by introducing anionic dyes to the positively charged self-assembled framework, which contained three luminescence centers, namely, pyrene, tpy-Cd coordination parts, and Sulforhodamine B anions. Such a hierarchically assembled system displayed tunable emission by taking full advantage of aggregation-induced emission enhancement, aggregation-caused quenching, and fluorescence resonance energy transfer effects and showed the diverse emission colors. This research provides a new insight for constructing multiple emissive metallo-supramolecular assemblies.

Advances in All-Inorganic Perovskite Nanocrystal-Based White Light Emitting Devices.

Metal halide perovskites (MHPs) are exceptional semiconductors best known for their intriguing properties, such as high absorption coefficients, tunable bandgaps, excellent charge transport, and high luminescence yields. Among various MHPs, all-inorganic perovskites exhibit benefits over hybrid compositions. Notably, critical properties, including chemical and structural stability, could be improved by employing organic-cation-free MHPs in optoelectronic devices such as solar cells and light-emitting devices (LEDs). Due to their enticing features, including spectral tunability over the entire visible spectrum with high color purity, all-inorganic perovskites have become a focus of intense research for LEDs. This Review explores and discusses the application of all-inorganic CsPbX3 nanocrystals (NCs) in developing blue and white LEDs. We discuss the challenges perovskite-based LEDs (PLEDs) face and the potential strategies adopted to establish state-of-the-art synthetic routes to obtain rational control over dimensions and shape symmetry without compromising the optoelectronic properties. Finally, we emphasize the significance of matching the driving currents of different LED chips and balancing the aging and temperature of individual chips to realize efficient, uniform, and stable white electroluminescence.

The Research Progress of Extraction, Purification and Analysis Methods of Phenolic Compounds from Blueberry: A Comprehensive Review.

Blueberry is the source of a variety of bioactive substances, including phenolic compounds, such as anthocyanins, pterostilbene, phenolic acids, etc. Several studies have revealed that polyphenols in blueberry have important bioactivities in maintaining health, such as antioxidant and anti-tumor activities, immune regulation, the prevention of chronic diseases, etc. Therefore, these phenolic compounds in blueberries have been widely used in the field of healthcare, and the extraction, isolation, and purification of phenolic compounds are the prerequisites for their utilization. It is imperative to systematically review the research progress and prospects of phenolic compounds present in blueberries. Herein, the latest progress in the extraction, purification, and analysis of phenolic compounds from blueberries is reviewed, which can in turn provide a foundation for further research and usage of blueberries.