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Abstract Endoplasmic reticulum (ER) stress has been shown to play a pivotal role in the pathogenesis of asthma. DEPTOR (DEP Domain Containing MTOR Interacting Protein) is an endogenous mTOR inhibitor that participates in various physiological processes such as cell growth, apoptosis, autophagy, and ER homeostasis. However, the role of DEPTOR in the pathogenesis of asthma is still unknown. In this study, an ovalbumin (OVA)-induced mice model and IL-13 induced 16HBE cells were used to evaluate the effect of DEPTOR on asthma. A decreased DEPTOR expression was shown in the lung tissues of OVA-mice and IL-13 induced 16HBE cells. Upregulation of DEPTOR attenuated airway goblet cell hyperplasia, inhibited mucus hypersecretion, decreased the expression of mucin MUC5AC, and suppressed the level of inflammatory factors IL-4 and IL-5, which were all induced by OVA treatment. The increased protein expression of ER stress markers GRP78, CHOP, unfolded protein response (UPR) related proteins, and apoptosis markers in OVA mice were also inhibited by DEPTOR overexpression. In IL-13 induced 16HBE cells, overexpression of DEPTOR decreased IL-4, IL-5, and MUC5AC levels, preventing ER stress response and UPR process. Furthermore, from the proteomics results, we identified that SOD1 (Cu/Zn Superoxide Dismutase 1) may be the downstream factor of DEPTOR. Similar to DEPTOR, upregulation of SOD1 alleviated asthma progression. Rescue experiments showed that SOD1 inhibition abrogates the remission effect of DEPTOR on ER stress in vitro. In conclusion, these data suggested that DEPTOR attenuates asthma progression by suppressing endoplasmic reticulum stress through SOD1.

Abstract Population studies have shown that the infant’s microbiome and metabolome undergo significant changes in early childhood. However, no previous study has investigated how diverse these changes are across subjects and whether the subject-specific dynamics of some microbes correlate with the over-time dynamics of specific metabolites. Using mixed-effects models, and data from the ABC study, we investigated the early childhood dynamics of fecal microbiome and metabolome and identified 83 amplicon sequence variants (ASVs) and 753 metabolites with seemingly coordinated trajectories. Enrichment analysis of these microbes and molecules revealed eight ASV families and 23 metabolite groups involving 1032 ASV-metabolite pairs with their presence-absence changing in a coordinated fashion. Members of the Lachnospiraceae (464/1032) and metabolites related to cholestane steroids (309/1032) dominated proportional shifts within the fecal microbiome and metabolome as infants aged.

Abstract Background Accurately identifying effective biomarkers and translating them into clinical practice have significant implications for improving clinical outcomes in hepatocellular carcinoma (HCC). In this study, our objective is to explore appropriate methods to improve the accuracy of biomarker identification and investigate their clinical value. Methods Concentrating on the N6-methyladenosine (m6A) modification regulators, we utilized dozens of multi-omics HCC datasets to analyze the expression patterns and genetic features of m6A regulators. Through the integration of big data analysis with function experiments, we have redefined the biological roles of m6A regulators in HCC. Based on the key regulators, we constructed m6A risk models and explored their clinical value in estimating prognosis and guiding personalized therapy for HCC. Results Most m6A regulators exhibit abnormal expression in HCC, and their expression is influenced by copy number variations (CNV) and DNA methylation. Large-scale data analysis has revealed the biological roles of many key m6A regulators, and these findings are well consistent with experimental results. The m6A risk models offer significant prognostic value. Moreover, they assist in reassessing the therapeutic potential of drugs such as sorafenib, gemcitabine, CTLA4 and PD1 blockers in HCC. Conclusions Our findings suggest that the mutual validation of big data analysis and functional experiments may facilitate the precise identification and definition of biomarkers, and our m6A risk models may have the potential to guide personalized chemotherapy, targeted treatment, and immunotherapy decisions in HCC.

Abstract Elderly individuals display metabolite alterations that may contribute to development of cognitive impairment following surgery and anesthesia. However, these relationships remain largely unexplored. The study aims to assess the S-methyl-5-thioadenosine (MTA) is associated with postoperative delayed neurocognitive recovery (dNCR). We assess altered metabolites following anesthesia/surgery in both mice and patients to identify blood biomarkers of dNCR. Preoperative and postoperative plasma metabolites are determined by widely targeted metabolomics. The brains of mice with anesthesia/surgery show decreased MTA and activated MTA phosphorylase. Mice also show that preoperative administration of MTA can prevent inflammation and cognitive decline. In clinical patients, we detect lower preoperative serum MTA levels in those who developed dNCR. Both low preoperative and postoperative blood MTA levels are associated with increased risk of postoperative dNCR. These results suggest that anesthesia/surgery induces cognitive decline through methionine synthesis pathways and that MTA could be a perioperative predictor of dNCR.

Abstract Single-cell RNA-sequencing (scRNA-seq) provides gene expression profiles of individual cells from complex samples, facilitating the detection of cell type-specific marker genes. In scRNA-seq experiments with multiple donors, the population level variation brings an extra layer of complexity in cell type-specific gene detection, for example, they may not appear in all donors. Motivated by this observation, we develop a statistical model named scCTS to identify cell type-specific genes from population-level scRNA-seq data. Extensive data analyses demonstrate that the proposed method identifies more biologically meaningful cell type-specific genes compared to traditional methods.

Abstract Increasingly, scRNA-Seq studies explore cell populations across different samples and the effect of sample heterogeneity on organism’s phenotype. However, relatively few bioinformatic methods have been developed which adequately address the variation between samples for such population-level analyses. We propose a framework for representing the entire single-cell profile of a sample, which we call a GloScope representation. We implement GloScope on scRNA-Seq datasets from study designs ranging from 12 to over 300 samples and demonstrate how GloScope allows researchers to perform essential bioinformatic tasks at the sample-level, in particular visualization and quality control assessment.

As natural bioactive compounds, plant pigments play crucial roles not only in plant phenotype, growth, development, and adaptation to stress but also hold unique value in biotechnology, healthcare, and industrial applications. There is growing interest in the biosynthesis and acquisition of plant pigments. Thus, this paper explores emerging extraction methods of natural pigments and elucidates the biosynthesis pathways of four key plant pigments, chlorophylls, carotenoids, anthocyanins, and betalaine in vivo and in vitro. We comprehensively discuss the application of solvent, supercritical fluid [extraction], ultrasonic, and microwave-assisted extraction techniques, as well as introducing key enzymes, precursors, and synthetic pathways involved in pigment synthesis. δ-Aminolevulinic acid represents a pivotal initiating enzyme for chlorophyll synthesis, whereas isopentenylpyrophosphate, (IPP) and dimethylallyl pyrophosphate, (DMAPP) are closely associated with carotenoid biosynthesis. Phenylalanine and tyrosine are critical substances for anthocyanin and betalaine synthesis, respectively. Hence, crucial genes such as chlI, crtB, PGT8, CYP76AD1, and BvDODA can be employed for heterologous biosynthesis in vitro to meet the demand for increased plant pigment amount. As a pivotal determinant of plant coloration, an in-depth exploration into the high-quality acquisition of plant pigments can provide a basis for developing superior pigments and offer new insights into increasing pigment yield.

Spheroids and organoids have attracted significant attention as innovative models for disease modeling and drug screening. By employing diverse types of spheroids or organoids, it is feasible to establish microphysiological systems that enhance the precision of disease modeling and offer more dependable and comprehensive drug screening. High-throughput microphysiological systems that support optional, parallel testing of multiple drugs have promising applications in personalized medical treatment and drug research. However, establishing such a system is highly challenging and requires a multidisciplinary approach. This study introduces a dynamic Microphysiological System Chip Platform (MSCP) with multiple functional microstructures that encompass the mentioned advantages. We developed a high-throughput lung cancer spheroids model and an intestine-liver-heart-lung cancer microphysiological system for conducting parallel testing on four anti-lung cancer drugs, demonstrating the feasibility of the MSCP. This microphysiological system combines microscale and macroscale biomimetics to enable a comprehensive assessment of drug efficacy and side effects. Moreover, the microphysiological system enables evaluation of the real pharmacological effect of drug molecules reaching the target lesion after absorption by normal organs through fluid-based physiological communication. The MSCP could serves as a valuable platform for microphysiological system research, making significant contributions to disease modeling, drug development, and personalized medical treatment.

Abstract Derived from enteroendocrine cells (EECs), glucagon-like peptide-1 (GLP-1) and glucose-dependent insulinotropic peptide (GIP) are pivotal incretin hormones crucial for blood glucose regulation. Medications of GLP-1 analogs and GLP-1 receptor activators are extensively used in the treatment of type 2 diabetes (T2D) and obesity. However, there are currently no agents to stimulate endogenous incretin secretion. Here, we find the pivotal role of KCNH2 potassium channels in the regulation of incretin secretion. Co-localization of KCNH2 with incretin-secreting EECs in the intestinal epithelium of rodents highlights its significance. Gut epithelial cell-specific KCNH2 knockout in mice improves glucose tolerance and increases oral glucose-triggered GLP-1 and GIP secretion, particularly GIP. Furthermore, KCNH2-deficient primary intestinal epithelial cells exhibit heightened incretin, especially GIP secretion upon nutrient stimulation. Mechanistically, KCNH2 knockdown in EECs leads to reduced K+ currents, prolonged action potential duration, and elevated intracellular calcium levels. Finally, we found that dofetilide, a KCNH2-specific inhibitor, could promote incretin secretion in enteroendocrine STC-1 cells in vitro and in hyperglycemic mice in vivo. These findings elucidate, for the first time, the mechanism and application of KCNH2 in regulating incretin secretion by EECs. Given the therapeutic promise of GLP-1 and GIP in diabetes and obesity management, this study advances our understanding of incretin regulation, paving the way for potential incretin secretagogue therapies in the treatment of diabetes and obesity.

Abstract Single-cell multi-omics data reveal complex cellular states, providing significant insights into cellular dynamics and disease. Yet, integration of multi-omics data presents challenges. Some modalities have not reached the robustness or clarity of established transcriptomics. Coupled with data scarcity for less established modalities and integration intricacies, these challenges limit our ability to maximize single-cell omics benefits. We introduce scCross, a tool leveraging variational autoencoders, generative adversarial networks, and the mutual nearest neighbors (MNN) technique for modality alignment. By enabling single-cell cross-modal data generation, multi-omics data simulation, and in silico cellular perturbations, scCross enhances the utility of single-cell multi-omics studies.

Abstract The emergence of single-cell Hi-C (scHi-C) technology has provided unprecedented opportunities for investigating the intricate relationship between cell cycle phases and the three-dimensional (3D) structure of chromatin. However, accurately predicting cell cycle phases based on scHi-C data remains a formidable challenge. Here, we present scHiCyclePred, a prediction model that integrates multiple feature sets to leverage scHi-C data for predicting cell cycle phases. scHiCyclePred extracts 3D chromatin structure features by incorporating multi-scale interaction information. The comparative analysis illustrates that scHiCyclePred surpasses existing methods such as Nagano_method and CIRCLET across various metrics including accuracy (ACC), F1 score, Precision, Recall, and balanced accuracy (BACC). In addition, we evaluate scHiCyclePred against the previously published CIRCLET using the dataset of complex tissues (Liu_dataset). Experimental results reveal significant improvements with scHiCyclePred exhibiting improvements of 0.39, 0.52, 0.52, and 0.39 over the CIRCLET in terms of ACC, F1 score, Precision, and Recall metrics, respectively. Furthermore, we conduct analyses on three-dimensional chromatin dynamics and gene features during the cell cycle, providing a more comprehensive understanding of cell cycle dynamics through chromatin structure. scHiCyclePred not only offers insights into cell biology but also holds promise for catalyzing breakthroughs in disease research. Access scHiCyclePred on GitHub at https:// github.com/HaoWuLab-Bioinformatics/ scHiCyclePred .

Abstract The peroxisome is a versatile organelle that performs diverse metabolic functions. PEX3, a critical regulator of the peroxisome, participates in various biological processes associated with the peroxisome. Whether PEX3 is involved in peroxisome-related redox homeostasis and myocardial regenerative repair remains elusive. We investigate that cardiomyocyte-specific PEX3 knockout (Pex3-KO) results in an imbalance of redox homeostasis and disrupts the endogenous proliferation/development at different times and spatial locations. Using Pex3-KO mice and myocardium-targeted intervention approaches, the effects of PEX3 on myocardial regenerative repair during both physiological and pathological stages are explored. Mechanistically, lipid metabolomics reveals that PEX3 promotes myocardial regenerative repair by affecting plasmalogen metabolism. Further, we find that PEX3-regulated plasmalogen activates the AKT/GSK3β signaling pathway via the plasma membrane localization of ITGB3. Our study indicates that PEX3 may represent a novel therapeutic target for myocardial regenerative repair following injury.

Objective This study investigates how astaxanthin (AST) counters tert-butyl hydroperoxide (tBHP)-induced cellular damage in C28/I2 chondrocytes, focusing on the circ-HP1BP3/miR-139-5p/SOD1 signaling pathway and its use in sustained-release microspheres for osteoarthritis treatment.Methods We employed a variety of techniques including real-time quantitative PCR, Western blot, ELISA, and dual-luciferase reporter gene assays to explore AST's molecular effects. Additionally, the efficacy of AST-loaded sustained-release microspheres was evaluated in vitro and in a mouse model of osteoarthritis.Results AST significantly enhanced SOD1 expression, reducing apoptosis and inflammation in damaged cells. The AST-loaded microspheres showed promising in vitro drug release, improved cell viability, and reduced oxidative stress. In the osteoarthritis mouse model, they effectively decreased joint inflammation and increased the expression of chondrocyte markers.Conclusion Astaxanthin effectively mitigates oxidative stress and inflammation in chondrocytes via the circ-HP1BP3/miR-139-5p/SOD1 pathway. The development of AST-loaded microspheres offers a novel and promising approach for osteoarthritis therapy, potentially extending to osteoarthritis treatment.

Calcium- and integrin-binding protein 1 (CIB1) has a diverse role in many different cell types and processes, including calcium signaling, migration, adhesion, proliferation, and survival. It is associated with cancer, cardiovascular disease and male infertility. Here, CRISPR/Cas9 genome-editing technology was employed to establish a CIB1 knockout human embryonic stem cell line, which exhibited normal pluripotency and karyotype.

SMALL AUXIN UP RNAs (SAURs), the largest family of early auxin response genes, plays crucial roles in multiple processes, including cell expansion, leaf growth and senescence, auxin transport, tropic growth and so on. Although the rice SAUR gene family was identified in 2006, it is necessary to identify the rice SAUR gene due to the imperfection of its analysis methods. In this study, a total of 60 OsSAURs (including two pseudogenes) distributed on 10 chromosomes were identified in rice (Oryza sativa). Bioinformatics tools were used to systematically analyze the physicochemical properties, subcellular localization, motif compositions, chromosomal location, gene duplication, evolutionary relationships, auxin-responsive cis-elements of the OsSAURs. In addition, the expression profiles obtained from microarray data analysis showed that OsSAUR genes had different expression patterns in different tissues and responded to auxin treatment, indicating functional differences among members of OsSAUR gene family. In a word, this study provides basic information for SAUR gene family of rice and lays a foundation for further study on the role of SAUR in rice growth and development.

Hypertrophic cardiomyopathy (HCM), characterized by left ventricular hypertrophy and preserved or increased left ventricular ejection fraction, is the most common autosomal dominant inherited cardiovascular disease. We generated a human induced pluripotent stem cell (hiPSC) line derived from a HCM patient who carried a heterozygous missense mutation in the myosin heavy chain 6 (MYH6) gene. With a non-integrated Sendai viral method, the patient-specific hiPSCs were generated from skin fibroblasts. We confirmed the stemness of the hiPSCs and its capability of differentiating into three germ layers. Meanwhile, the generated hiPSCs showed human embryonic stem cell-like morphology and normal karyotype.

To investigate the synergistic effect of IAA and melatonin (MT) on three plants to alleviate the effects of salt damage on plants, we aim to determine the optimal concentrations of exogenous hormone treatments that improve salinity resistance for each species. In this experiment, three desert plants, Sarcozygium xanthoxylon, Nitraria tangutorum, and Ammopiptanthus mongolicus, which are common in Wuhai City, were used as plant materials. Two time periods (12 h,24 h) of exogenous hormone IAA (100 μmol/L) and exogenous melatonin concentration (0, 100, 200, 300 μmol/L) were used to treat the three desert plants in saline soil under different conditions of exogenous IAA and exogenous melatonin. The results indicate that under different concentrations of exogenous IAA and melatonin, the germination rate and vigor of the three desert plant species in saline-alkaline soil improved. However, as the concentration of melatonin increased, the germination rate and vigor of these desert plants were inhibited. Whereas, plant height, root length, leaf length, fresh weight, dry weight, and root vigor of the three desert plants were alleviated under different conditions of exogenous IAA and exogenous melatonin. under the action of two exogenous hormones, the low concentration of melatonin decreased their malondialdehyde content and increased their proline content. As melatonin levels increased, the activity of antioxidant enzymes also rose initially, followed by a subsequent decline. This study highlights the synergistic effects of two exogenous hormones on the critical role of cell osmomodulators and antioxidant enzyme activity in combating salinity damage in three desert plants.

Background Currently, endoscopic transsphenoidal surgery is the primary approach for treating pituitary tumors. While endoscopic surgery offers numerous advantages, it also comes with a series of potential surgical complications. Postoperative hypokalemia is a common complication, with mild cases presenting with atypical symptoms such as dizziness, headache, fatigue, and constipation, while severe cases can lead to arrhythmias, rhabdomyolysis, and even death. Therefore, early identification of risk factors for postoperative hypokalemia is crucial. This study aims to analyze the risk factors for hypokalemia after endoscopic pituitary tumor resection. Methods and Materials This study included 168 patients who underwent endoscopic resection of pituitary tumors between 2019 and 2023. Patients were divided into hypokalemia group and non-hypokalemia group based on whether their postoperative serum potassium concentration was less than 3.0 mEq/L. Identifying independent risk factors through binary logistic regression analysis. Results Among the 168 patients, 18 (10.7%) cases experienced postoperative hypokalemia, with the majority occurring on the fourth day after surgery. The majority of patients did not exhibit clinical symptoms related to hypokalemia. The binary logistic regression analysis revealed that age (OR 1.09; 95% CI [1.03–1.15]; P = 0.001) and postoperative hypoalbuminemia on the first day (OR, 4.35; 95% CI [1.38–13.75]; P = 0.012) were associated with postoperative hypokalemia. Conclusions Patients aged ≥50 years and those presenting with hypoalbuminemia on the first postoperative day were more likely to develop postoperative hypokalemia. Therefore, electrolyte monitoring should be enhanced in such patients postoperatively, especially to actively prevent hypokalemia on the 4th–5th postoperative day.

Brugada syndrome (BrS) is a hereditary arrhythmia syndrome characterized by right bundle branch block on an electrocardiogram and persistent ST-segment elevation in the right precordial leads. In this study, we describe the establishment of an induced pluripotent stem cell (iPSC) line derived from a BrS patient carrying the novel heterogeneous missense mutation (c.3118G>C; p.G1040R) in the sodium channel protein type 5 subunit alpha (SCN5A) gene. Skin fibroblasts underwent reprogramming using a non-integrated Sendai viral method. Generated iPSC line exhibited embryonic stem cell-like morphology, maintained a normal karyotype, expressed pluripotency markers, and demonstrated the capacity to differentiate into three germ layers.

Abstract Therapeutic agents targeting cytokine-cytokine receptor (CK-CKR) interactions lead to the disruption in cellular signaling and are effective in treating many diseases including tumors. However, a lack of universal and quick access to annotated structural surface regions on CK/CKR has limited the progress of a structure-driven approach in developing targeted macromolecular drugs and precision medicine therapeutics. Herein we develop CytoSIP (Single nucleotide polymorphisms (SNPs), Interface, and Phenotype), a rich internet application based on a database of atomic interactions around hotspots in experimentally determined CK/CKR structural complexes. CytoSIP contains: (1) SNPs on CK/CKR; (2) interactions involving CK/CKR domains, including CK/CKR interfaces, oligomeric interfaces, epitopes, or other drug targeting surfaces; and (3) diseases and phenotypes associated with CK/CKR or SNPs. The database framework introduces a unique tri-level SIP data model to bridge genetic variants (atomic level) to disease phenotypes (organism level) using protein structure (complexes) as an underlying framework (molecule level). Customized screening tools are implemented to retrieve relevant CK/CKR subset, which reduces the time and resources needed to interrogate large datasets involving CK/CKR surface hotspots and associated pathologies. CytoSIP portal is publicly accessible at https://CytoSIP.biocloud.top , facilitating the panoramic investigation of the context-dependent crosstalk between CK/CKR and the development of targeted therapeutic agents.

Abstract Ca2+/calmodulin-dependent protein kinase II (CaMKII) is a family of broad substrate specificity serine (Ser)/threonine (Thr) protein kinases that play a crucial role in the Ca2+-dependent signaling pathways. Its significance as an intracellular Ca2+ sensor has garnered abundant research interest in the domain of neurodegeneration. Accumulating evidences suggest that CaMKII is implicated in the pathology of degenerative retinopathies such as diabetic retinopathy (DR), age-related macular degeneration (AMD), retinitis pigmentosa (RP) and glaucoma optic neuropathy. CaMKII can induce the aberrant proliferation of retinal blood vessels, influence the synaptic signaling, and exert dual effects on the survival of retinal ganglion cells and pigment epithelial cells. Researchers have put forth multiple therapeutic agents, encompassing small molecules, peptides, and nucleotides that possess the capability to modulate CaMKII activity. Due to its broad range isoforms and splice variants therapeutic strategies seek to inhibit specifically the CaMKII are confronted with considerable challenges. Therefore, it becomes crucial to discern the detrimental and advantageous aspects of CaMKII, thereby facilitating the development of efficacious treatment. In this review, we summarize recent research findings on the cellular and molecular biology of CaMKII, with special emphasis on its metabolic and regulatory mechanisms. We delve into the involvement of CaMKII in the retinal signal transduction pathways and discuss the correlation between CaMKII and calcium overload. Furthermore, we elaborate the therapeutic trials targeting CaMKII, and introduce recent developments in the zone of CaMKII inhibitors. These findings would enrich our knowledge of CaMKII, and shed light on the development of a therapeutic target for degenerative retinopathy.

Abstract Ossification of the Posterior Longitudinal Ligament (OPLL) is a degenerative hyperostosis disease characterized by the transformation of the soft and elastic vertebral ligament into bone, resulting in limited spinal mobility and nerve compression. Employing both bulk and single-cell RNA sequencing, we elucidate the molecular characteristics, cellular components, and their evolution during the OPLL process at a single-cell resolution, and validate these findings in clinical samples. This study also uncovers the capability of ligament stem cells to exhibit endothelial cell-like phenotypes in vitro and in vivo. Notably, our study identifies LOXL2 as a key regulator in this process. Through gain-and loss-of-function studies, we elucidate the role of LOXL2 in the endothelial-like differentiation of ligament cells. It acts via the HIF1A pathway, promoting the secretion of downstream VEGFA and PDGF-BB. This function is not related to the enzymatic activity of LOXL2. Furthermore, we identify sorafenib, a broad-spectrum tyrosine kinase inhibitor, as an effective suppressor of LOXL2-mediated vascular morphogenesis. By disrupting the coupling between vascularization and osteogenesis, sorafenib demonstrates significant inhibition of OPLL progression in both BMP-induced and enpp1 deficiency-induced animal models while having no discernible effect on normal bone mass. These findings underscore the potential of sorafenib as a therapeutic intervention for OPLL.

Given post-operative aseptic loosening in orthopedic disease treatment, osteointegration occurs at the bone-implant interface as a holistic process, including immunoregulation (e.g., macrophage polarization), angiogenesis and osteogenesis in sequence. In order to achieve early rapid and satisfactory osseointegration, different nano-shaped (nanocone, nanopolyhedron and nanoflower abbr. NC, NP & NF) cerium oxide (CeO2-x) coatings, endowed with “nanozyme-like” activities for multiple free radical elimination and osteoimmunology regulation, were hydrothermally synthesized on titanium alloy (TC4). In vitro cell experiments showed that nano-CeO2-x coated TC4 not only induced polarization of RAW264.7 cells toward M2 phenotype, but also promoted angiogenesis and vascularization of endothelial cells along with differentiation and mineralization of osteogenic precursor cells. Improvements in M2-polarized macrophage, angiogenesis, and bone regeneration were further confirmed in a rat femoral condyle model. Among the above three nano-morphologies, NF exhibited the best osseoinetegration. RNA sequencing and mechanism exploration suggested that the inhibition of PI3K-AKT signaling pathway was essential for immunomodulatory capacity of NF. In conclusion, it provided promising insights into the immunomodulatory exploitation of orthopedic implants.

Ethylamine (EA), the precursor of theanine biosynthesis, is synthesized from alanine decarboxylation by alanine decarboxylase (AlaDC) in tea plants. AlaDC evolves from serine decarboxylase (SerDC) through neofunctionalization and has lower catalytic activity. However, lacking structure information hinders the understanding of the evolution of substrate specificity and catalytic activity. In this study, we solved the X-ray crystal structures of AlaDC from Camellia sinensis (CsAlaDC) and SerDC from Arabidopsis thaliana (AtSerDC). Tyr341 of AtSerDC or the corresponding Tyr336 of CsAlaDC is essential for their enzymatic activity. Tyr111 of AtSerDC and the corresponding Phe106 of CsAlaDC determine their substrate specificity. Both CsAlaDC and AtSerDC have a distinctive zinc finger and have not been identified in any other Group II PLP-dependent amino acid decarboxylases. Based on the structural comparisons, we conducted a mutation screen of CsAlaDC. The results indicated that the mutation of L110F or P114A in the CsAlaDC dimerization interface significantly improved the catalytic activity by 110% and 59%, respectively. Combining a double mutant of CsAlaDCL110F/P114A with theanine synthetase increased theanine production 672% in an in vitro system. This study provides the structural basis for the substrate selectivity and catalytic activity of CsAlaDC and AtSerDC and provides a route to more efficient biosynthesis of theanine.

Background: We aimed to contrast plasma amino acid concentrations in pregnant women with Gestational Diabetes Mellitus (GDM) to those without, to analyze the link between plasma amino acid concentrations, GDM, insulin resistance, and insulin secretion at 24–28 weeks of gestation. Methods: The research employed a retrospective case-control study design at a single center. Basic demographic and laboratory data were procured from the hospital's case system. The study encompassed seventy women without gestational diabetes mellitus (GDM) and thirty-five women with GDM matched in a 1-to-2 ratio for age and pre-pregnancy BMI. Utilizing high-performance liquid chromatography-mass spectrometry (HPLC-MS), peripheral fasting plasma amino acid concentrations in these women, during mid-pregnancy, were duly measured. We carefully evaluated the significant differences in the quantitative data between the two groups and developed linear regression models to assess the independent risk factors affecting insulin resistance and insulin secretion. Results: Significant variations in insulin secretion and resistance levels distinguished GDM Group from the non-GDM group at three distinct time points, alongside relatively elevated serum Glycosylated Hemoglobin (HbA1c) levels. Triglycerides (TG) were also significantly increased in those with GDM during adipocytokine observations. Apart from glutamic acid and glutamine, the concentrations of the remaining 16 amino acids were notably increased in GDM patients, including all branched chain amino acids(BCAAs) and aromatic amino acids(AAAs). Ultimately, it was ascertained that fasting serum phenylalanine levels were independent risk factors affecting insulin resistance index and insulin secretion at various phases. Conclusions: Various fasting serum amino acid levels are markedly increased in patients with GDM, specifically phenylalanine, which may play role in insulin resistance and secretion.

Bathymodioline mussels dominate deep-sea methane seep and hydrothermal vent habitats and obtain nutrients and energy primarily through chemosynthetic endosymbiotic bacteria in the bacteriocytes of their gill. However, the molecular mechanisms that orchestrate mussel host–symbiont interactions remain unclear. Here, we constructed a comprehensive cell atlas of the gill in the mussel Gigantidas platifrons from the South China Sea methane seeps (1100 m depth) using single-nucleus RNA-sequencing (snRNA-seq) and whole-mount in situ hybridisation. We identified 13 types of cells, including three previously unknown ones, and uncovered unknown tissue heterogeneity. Every cell type has a designated function in supporting the gill’s structure and function, creating an optimal environment for chemosynthesis, and effectively acquiring nutrients from the endosymbiotic bacteria. Analysis of snRNA-seq of in situ transplanted mussels clearly showed the shifts in cell state in response to environmental oscillations. Our findings provide insight into the principles of host–symbiont interaction and the bivalves' environmental adaption mechanisms.

Posterior segment disease acts as a major cause of irreversible visual impairments. Successful treatment of posterior segment disease requires the efficient delivery of therapeutic substances to the targeted lesion. However, the complex ocular architecture makes the bioavailability of topically applied drugs extremely low. Invasive delivery approaches like intravitreal injection may cause adverse complications. To enhance the efficiency, several biomedical engineering systems have been developed to increase the penetration efficiency and improve the bioavailability of drugs at the posterior segments. Advantageously, biodegradable microspheres are found to deliver the therapeutic agents in a controlled fashion. The microspheres prepared from novel biomaterials can realize the prolonged release at the posterior segment with minimum side effects. Moreover, it will be degraded automatically into products that are non-toxic to the human body without the necessity of secondary operation to remove the residual polymer matrix. Additionally, biodegradable microspheres have decent thermoplasticity, adjustable hydrophilicity, controlled crystallinity, and high tensile strength, which make them suitable for intraocular delivery. In this review, we introduce the latest advancements in microsphere production technology and elaborate on the biomaterials that are used to prepare microspheres. We discuss systematically the pharmacological characteristics of biodegradable microspheres and compare their potential advantages and limitations in the treatment of posterior segment diseases. These findings would enrich our knowledge of biodegradable microspheres and cast light into the discovery of effective biomaterials for ocular drug delivery.

Introduction: Biocatalysis, particularly through engineered enzymes, presents a cost-effective, efficient, and eco-friendly approach to compound synthesis. We sought to identify ketoreductases capable of synthesizing optically pure alcohols or ketones, essential chiral building blocks for active pharmaceutical ingredients.Methods: Using BioMatchMaker®, an in silico high-throughput platform that allows the identification of wild-type enzyme sequences for a desired chemical transformation, we identified a bacterial SDR ketoreductase from Thermus caliditerrae, Tcalid SDR, that demonstrates favorable reaction efficiency and desired enantiomeric excess.Results: Here we present two crystal structures of the Tcalid SDR in an apo-form at 1.9 Å and NADP-complexed form at 1.7 Å resolution (9FE6 and 9FEB, respectively). This enzyme forms a homotetramer with each subunit containing an N-terminal Rossmann-fold domain. We use computational analysis combined with site-directed mutagenesis and enzymatic characterization to define the substrate-binding pocket. Furthermore, the enzyme retained favorable reactivity and selectivity after incubation at elevated temperature.Conclusion: The enantioselectivity combined with the thermostability of Tcalid SDR makes this enzyme an attractive engineering starting point for biocatalysis applications.

Bacterial exonuclease III (ExoIII), widely acknowledged for specifically targeting double-stranded DNA (dsDNA), has been documented as a DNA repair-associated nuclease with apurinic/apyrimidinic (AP)-endonuclease and 3′→5′ exonuclease activities. Due to these enzymatic properties, ExoIII has been broadly applied in molecular biosensors. Here, we demonstrate that ExoIII (Escherichia coli) possesses highly active enzymatic activities on ssDNA. By using a range of ssDNA fluorescence-quenching reporters and fluorophore-labeled probes coupled with mass spectrometry analysis, we found ExoIII cleaved the ssDNA at 5′-bond of phosphodiester from 3′ to 5′ end by both exonuclease and endonuclease activities. Additional point mutation analysis identified the critical residues for the ssDNase action of ExoIII and suggested the activity shared the same active center with the dsDNA-targeted activities of ExoIII. Notably, ExoIII could also digest the dsDNA structures containing 3′-end ssDNA. Considering most ExoIII-assisted molecular biosensors require the involvement of single-stranded DNA (ssDNA) or nucleic acid aptamer containing ssDNA, the activity will lead to low efficiency or false positive outcome. Our study revealed the multi-enzymatic activity and the underlying molecular mechanism of ExoIII on ssDNA, illuminating novel insights for understanding its biological roles in DNA repair and the rational design of ExoIII-ssDNA involved diagnostics.

Abstract Cellular metabolism is an intricate network satisfying bioenergetic and biosynthesis requirements of cells. Relevant studies have been constantly making inroads in our understanding of pathophysiology, and inspiring development of therapeutics. As a crucial component of epigenetics at post-transcription level, RNA modification significantly determines RNA fates, further affecting various biological processes and cellular phenotypes. To be noted, immunometabolism defines the metabolic alterations occur on immune cells in different stages and immunological contexts. In this review, we characterize the distribution features, modifying mechanisms and biological functions of 8 RNA modifications, including N6-methyladenosine (m6A), N6,2′-O-dimethyladenosine (m6Am), N1-methyladenosine (m1A), 5-methylcytosine (m5C), N4-acetylcytosine (ac4C), N7-methylguanosine (m7G), Pseudouridine (Ψ), adenosine-to-inosine (A-to-I) editing, which are relatively the most studied types. Then regulatory roles of these RNA modification on metabolism in diverse health and disease contexts are comprehensively described, categorized as glucose, lipid, amino acid, and mitochondrial metabolism. And we highlight the regulation of RNA modifications on immunometabolism, further influencing immune responses. Above all, we provide a thorough discussion about clinical implications of RNA modification in metabolism-targeted therapy and immunotherapy, progression of RNA modification-targeted agents, and its potential in RNA-targeted therapeutics. Eventually, we give legitimate perspectives for future researches in this field from methodological requirements, mechanistic insights, to therapeutic applications.

Abstract Neurotransmitter-initiated signaling pathway were reported to play an important role in regulating the malignant phenotype of tumor cells. Cancer cells could exhibit a “neural addiction” property and build up local nerve networks to achieve an enhanced neurotransmitter-initiated signaling through nerve growth factor-mediated axonogenesis. Targeting the dysregulated nervous systems might represent a novel strategy for cancer treatment. However, whether intrahepatic cholangiocarcinoma (ICC) could build its own nerve networks and the role of neurotransmitters in the progression ICC remains largely unknown. Immunofluorescence staining and Enzyme-linked immunosorbent assay suggested that ICC cells and the infiltrated nerves could generate a tumor microenvironment rich in acetylcholine that promotes ICC metastasis by inducing epithelial-mesenchymal transition (EMT). Acetylcholine promoted ICC metastasis through interacting with its receptor, alpha 5 nicotine acetylcholine receptor subunits (CHRNA5). Furthermore, acetylcholine/CHRNA5 axis activated GSK3β/β-catenin signaling pathway partially through the influx of Ca2+-mediated activation of Ca/calmodulin-dependent protein kinases (CAMKII). In addition, acetylcholine signaling activation also expanded nerve infiltration through increasing the expression of Brain-Derived Neurotrophic Factor (BDNF), which formed a feedforward acetylcholine-BDNF axis to promote ICC progression. KN93, a small-molecule inhibitor of CAMKII, significantly inhibited the migration and enhanced the sensitivity to gemcitabine of ICC cells. Above all, Acetylcholine/CHRNA5 axis increased the expression of β-catenin to promote the metastasis and resistance to gemcitabine of ICC via CAMKII/GSK3β signaling, and the CAMKII inhibitor KN93 may be an effective therapeutic strategy for combating ICC metastasis.

Abstract Long-term use of glucocorticoids (GCs) is known to be a predominant cause of osteonecrosis of the femoral head (ONFH). Moreover, GCs can mediate apoptosis of various cell types by exaggerating oxidative stress. We have previously found that Cortistatin (CST) antagonizes oxidative stress and improves cell apoptosis in several conditions. In this study, we detected that the CST expression levels were diminished in patients with ONFH compared with femoral neck fracture (FNF). In addition, a GC-induced rat ONFH model was established, which impaired bone quality in the femoral head. Then, administration of CST attenuated these ONFH phenotypes. Furthermore, osteoblast and endothelial cells were cultured and stimulated with dexamethasone (Dex) in the presence or absence of recombinant CST. As a result, Dex induced impaired anabolic metabolism of osteoblasts and suppressed tube formation in endothelial cells, while additional treatment with CST reversed this damage to the cells. Moreover, blocking GHSR1a, a well-accepted receptor of CST, or blocking the AKT signaling pathway largely abolished the protective function of CST in Dex-induced disorder of the cells. Taken together, we indicate that CST has the capability to prevent GC-induced apoptosis and metabolic disorder of osteoblasts in the pathogenesis of ONFH via the GHSR1a/AKT signaling pathway.

The cohesive properties of lunar regolith, combined with a low-gravity environment, result in it having a distinct mechanical behavior from sandy soil on Earth. Consequently, empirical formulas derived from cone penetration tests (CPTs) for calculating the shear strength parameters of Earth’s sand cannot be directly applied to lunar regolith. This study utilized the three-dimensional discrete element method (DEM) to numerically simulate triaxial shear tests and cone penetration tests in a lunar environment. The particle contact model for lunar regolith in the discrete element method (DEM) simulation incorporated the hysteresis effect of van der Waals forces, thereby simulating the cohesive properties of lunar regolith in a lunar environment. We proposed a relationship for calculating the shear strength index of lunar regolith based on normalized cone tip resistance using the results from triaxial and CPT simulations and referencing empirical formulas derived from ground-based CPT data. The results of this study provide a valuable reference for future lunar CPTs.

The cultivation of Fritillaria ussuriensis faces challenges due to the prevalent Fritillaria wilt disease, hindering large-scale production. To address this, we aimed to understand the disease’s characteristics and develop effective prevention measures. Microbial communities of diseased F. ussuriensis plants were analyzed, pathogenic and antagonistic strains were screened, and biocontrol feasibility was tested. We identified Botryotinia predominance in aboveground parts and variations in Mrakia, Humicola, llyonectria, and Fusarium in underground parts. The pathogens Fusarium oxysporum IFM-1 and Fusarium solani IFM-52 isolated from diseased F. ussuriensis not only caused severe Fritillaria wilt but were also pathogenic to Lilium lancifolium and Allium cepa var. aggregatum in Liliaceae. The antagonistic Bacillus tequilensis LFM-30 and Trichoderma koningiopsis IFM-47 isolated from diseased plants significantly alleviated plant wilt and showed promise in preventing wilt disease caused by Fusarium in Liliaceae plants. Our study highlights distinct microbial differences between healthy and diseased F. ussuriensis and underscores the pathogenicity of Fusarium. Using T. koningiopsis and B. tequilensis either singly or in combination could offer effective biocontrol against F. solani and F. oxysporum, benefiting F. ussuriensis and related Liliaceae plants.

Parasitic infestations present significant threats to the physiological health and ecological stability of aquatic species, frequently compromising immune defenses and elevating mortality rates. This study was conducted to elucidate the non-specific immune responses induced by Pallisentis (Neosentis) celatus infection in Monopterus albus, with a focus on intestinal histopathology and transcriptome gene expression. A histopathological examination revealed minor alterations in intestinal villi under low-level infection. A transcriptome analysis, performed using Illumina sequencing technology, identified 347 upregulated and 298 downregulated genes involved in critical biological pathways, such as lipid metabolism, immune responses, and the regulation of inflammatory processes. GO and KEGG analyses indicated the upregulation of immune-related pathways, including the RIG-I-like and IL-17 signaling pathways, highlighting a robust intestinal immune response. Conversely, the complement pathway was found to be downregulated, with significant suppression of C9, suggesting that the parasite may engage in immune evasion. Fluorescein-labeled C9 antibody assays confirmed reduced complement C9 levels in the infected tissues. A real-time PCR analysis identified the differential expression of eight genes, including C5, maats1, CFI, and gmnc, which were consistent with the sequencing results. These findings suggest that Pallisentis (Neosentis) celatus infection compromises intestinal health, induces inflammation, and activates non-specific immune responses in Monopterus albus. However, Pallisentis (Neosentis) celatus appears to evade the host immune response by suppressing the activation of complement components, thereby facilitating its reproductive parasitism.

Abdominal CT images are important clues for diagnosing liver cancer lesions. However, liver cancer presents challenges such as significant differences in tumor size, shape, and location, which can affect segmentation accuracy. To address these challenges, we propose an end-to-end 3D segmentation algorithm, RMCNet. In the shallow encoding part of RMCNet, we incorporated a 3D multiscale convolution (3D-Multiscale Convolution) module to more effectively extract tumors of varying sizes. Moreover, the convolutional block attention module (CBAM) is used in the encoding part to help the model focus on both the shape and location of tumors. Additionally, a residual path is introduced in each encoding layer to further enrich the extracted feature maps. Our method achieved DSC scores of 76.56% and 72.96%, JCC scores of 75.82% and 71.25%, HD values of 11.07 mm and 17.06 mm, and ASD values of 2.54 mm and 10.51 mm on the MICCAI 2017 Liver Tumor Segmentation public dataset and the 3Dircadb-01 public dataset, respectively. Compared to other methods, RMCNet demonstrates superior segmentation performance and stronger generalization capability.

Docetaxel has exhibited excellent therapeutic effects in cancer treatment; however, its hydrophobicity, short blood circulation time, and high blood toxicity restrict its clinical application. The use of mPEG-PLA micelles to deliver docetaxel into the body has been verified as an effective approach to enhance its therapeutic efficacy. However, mPEG-PLA micelles are easily disassembled in the bloodstream, which can easily lead to premature drug release. To broaden the application scenarios of mPEG PLA micelles, we utilized the π–π stacking effect as an intermolecular force to design a novel mPEG-PLA-Lys(Fmoc) micelle to enhance the blood stability and permeability of drug-loaded micelles. The result showed that drug-loaded micelles for injection did not alter the tissue selectivity of docetaxel. Intravenous injection of the micelles in nude mice showed better antitumor efficacy than docetaxel injection and tumor recurrence rate is 0%, which is significantly lower than that of docetaxel injection (100%). The micelles designed by this research institute are anticipated to improve the clinical therapeutic effect of docetaxel.

Fish gut health is influenced by various factors, with the environment being a significant one. S. sinensis is a key aquaculture species in China, yet research on the impact of different aquaculture systems on its intestinal health remains limited. This study aims to explore the changes in intestinal morphology and gut microbiota of S. sinensis under two aquaculture systems. The juveniles of S. sinensis were divided into two groups and cultured in traditional ponds (CT) and an in-pond tank culture system (JY), with equal amounts of feed provided daily over a 72-day experimental period. The results showed no significant differences in growth performance metrics, including the specific growth rate, weight gain rate, hepatosomatic index, and viscerosomatic index between the two groups. In terms of intestinal morphology, the JY group villus width was significantly wider than the CT group, and the number of goblet cells in the CT group was significantly higher than that of the JY group (p < 0.05), which suggested that the fish in the JY group may have better intestinal nutrient absorption capacity, while the water quality in the CT group may be worse. The 16S rRNA gene sequencing analysis of the gut microbiota showed that the JY group had a significantly higher Shannon index compared to the CT group (p < 0.05), indicating greater species richness and evenness. Principal Coordinates Analysis (PCoA) revealed a distinct clustering of gut microbiota between the two groups. At the phylum level, the relative abundance of Fusobacteriota was significantly higher in the CT group, whereas Bacteroidota and Proteobacteria were significantly higher in the JY group (p < 0.05). Furthermore, KEGG pathway predictions indicated differences in the potential metabolic capabilities of the gut microbiota between the two groups (p < 0.05). Overall, this study is the first to conduct a comparative analysis of the growth performance, intestinal tissue morphology, and gut microbiota of S. sinensis under two different aquaculture systems, which has valuable implications for the further optimization of aquaculture practices.

The shear band is a prominent feature within the Banbiyan hazardous rock mass located in the Wushan section of the Three Gorges Reservoir area. This band constitutes a latent risk, as the potential for the rock mass to slide along the region threatens the safety of lives and property. Presently, the understanding of the shear mechanisms and the impact of shear band size on the band–bedrock interface is incomplete. In this study, based on band–bedrock shear laboratory tests, DEM simulation is used to investigate the shear-induced coalescence mechanism, stress evolution, and crack-type characteristics of the band–bedrock interface. In addition, the shear mechanical properties of samples considering specimen size, rock step height, and step width are further studied. The results show that the crack initiation and failure crack types observed in the first rock step are predominantly tensile. In contrast, the failure cracks in the remaining rock slabs and steps are primarily characterised by shear mode in addition to other mixed modes. The stress condition experienced by the first step is very near to the position of the applied point load, whereas the stress distribution across the remaining steps shows a more complex state of compressive–tensile stress. The relationship between shear parameters and sample size is best described by a negative exponential function. The representative elementary volume (REV) for shear parameters is suggested to be a sample with a geometric size of 350 mm. Notably, the peak shear strength and shear elastic modulus demonstrate a progressive increase with the rise in rock step height, with the amplifications reaching 91.37% and 115.83%, respectively. However, the residual strength exhibits an initial decline followed by a gradual ascent with increasing rock step height, with the amplitude of reduction and subsequent amplification being 23.73% and 116.94%, respectively. Additionally, a narrower rock step width is found to diminish the shear parameter values, which then tend to stabilise within a certain range as the step width increases.

Background: Myocardial Infarction (MI) and severe mental disorders (SMDs) are two types of highly prevalent and complex disorders and seem to have a relatively high possibility of mortality. However, the contributions of common and rare genetic variants to their comorbidity arestill unclear. Methods: We conducted a combined genome-wide association study (GWAS) and exome-wide association study (EWAS) approach. Results: Using gene-based and gene-set association analyses based on the results of GWAS, we found the common genetic underpinnings of nine genes (GIGYF2, KCNJ13, PCCB, STAG1, HLA-C, HLA-B, FURIN, FES, and SMG6) and nine pathways significantly shared between MI and SMDs. Through Mendelian randomization analysis, we found that twenty-seven genes were potential causal genes for SMDs and MI. Based on the exome sequencing data of MI and SMDs patients from the UK Biobank, we found that MUC2 was exome-wide significant in the two diseases. The gene-set analyses of the exome-wide association study indicated that pathways related to insulin processing androgen catabolic process and angiotensin receptor binding may be involved in the comorbidity between SMDs and MI. We also found that six candidate genes were reported to interact with known therapeutic drugs based on the drug–gene interaction information in DGIdb. Conclusions: Altogether, this study revealed the overlap of common and rare genetic underpinning between SMDs and MI and may provide useful insights for their mechanism study and therapeutic investigations.

Currently, the primary method for controlling red tides in the ocean involves spraying water solutions with special chemicals as solutes. High-pressure spraying results in the formation of typical jet structures. In this study, numerical simulation methods are employed to investigate the velocity variations, turbulent characteristics, and gas content distribution of jet flow fields under different initial jet flow pressures, cone angles, and nozzle diameters. Based on practical application scenarios, cluster analysis is used to explore the similarities and differences in jet equivalent diameters under different parameter conditions. The research findings indicate the following. (1) The difference of jet velocity distribution at the far field exit will be enlarged with the increase in the nozzle cone angle. When the nozzle cone angle is 4 mm, the velocity uniformity at the outlet is the best. (2) The TKE of the flow field has no consistent change law along the central axis. At the jet exit, the TKE shows an obvious multi-peak structure. (3) The gas content demonstrates a typical “double-valley” feature at the jet outlet cross-section. Increasing the initial pressure leads to a decrease in the gas content within the jet due to reduced entrainment, while the entrainment range remains largely constant. (4) Cluster analysis reveals that the similarity of jet flow width when it reaches the water surface is minimal compared to other operating conditions when the initial pressure is 0.36 MPa, the cone angle is 115°, and the nozzle diameter is 2 mm. All conditions can be categorized into two or three groups to ensure jet effectiveness. The study results provide scientific guidance for selecting spray devices for controlling red tides in the ocean.

Various hydrogeological problems like groundwater inflow, water table drawdown, and water pressure redistribution may be encountered in the construction of hydraulic projects. How to accurately predict the occurrence of groundwater inflow and assess the drainage effect during construction are still challenging problems for engineering designers. Taking the Jinzhai pumped storage power station (JPSPS) of China as an example, this paper aims to use different methods to calculate the water inflow rates of an underground powerhouse and evaluate the drainage effect caused by tunnel inflow during construction. The methods consist of the analytical formulas, the site groundwater rating (SGR) method, and the Signorini type variational inequality formulation. The results show that the analytical methods considering stable water table may overestimate the water inflow rates of caverns in drained conditions, whereas the SGR method with available hydro-geological parameters obtains a qualitative hazard assessment in the preliminary phase. The numerical solutions provide more precise and reliable values of groundwater inflow considering complex geological structures and seepage control measures. Moreover, the drainage effects, including a seepage-free surface, pore water pressure redistribution, and hydraulic gradient, have been accurately evaluated using various numerical synthetic cases. Specifically, the faults intersecting on underground caverns and drainage structures significantly change the groundwater flow regime around caverns. This comparative study can not only exactly identify the capabilities of the methods for cavern inflow in drained conditions, but also can comprehensively evaluate the drainage effect during cavern construction.

IntroductionAcetyl-CoA synthetase 2 (ACSS2), one of the enzymes that catalyze the conversion of acetate to acetyl-CoA, has been proved to be an oncogene in various cancers. However, the function of ACSS2 is still largely a black box in melanoma.MethodsThe ACSS2 expression was detected in melanoma cells and melanocytes at both protein and mRNA levels. Cell viability, apoptosis, migration and invasion were investigated after ACSS2 knockdown. RNA sequencing (RNA-Seq) technology was employed to identify differentially expressed genes caused by ACSS2 knockdown, which were then verified by immunoblotting analysis. Animal experiments were further performed to investigate the influence of ACSS2 on tumor growth and metastasis in vivo.ResultsFirstly, we found that ACSS2 was upregulated in most melanoma cell lines compared with melanocytes. In addition, ACSS2 knockdown dramatically suppressed melanoma cell migration and invasion, whereas promoted cell apoptosis in response to endoplasmic reticulum (ER) stress. Furthermore, tumor growth and metastasis were dramatically suppressed by ACSS2 knockdown in vivo. RNA-Seq suggested that the Hippo pathway was activated by ACSS2 knockdown, which was forwardly confirmed by Western blotting and rescue experiments. Taken together, we demonstrated that ACSS2 enables melanoma cell survival and tumor metastasis via the regulation of the Hippo pathway.DiscussionIn summary, this study demonstrated that ACSS2 may promote the growth and metastasis of melanoma by negatively regulating the Hippo pathway. Targeting ACSS2 may be a promising target for melanoma treatment.

Owing to the tissue characteristics of tendons with few blood vessels and cells, the regeneration and repair of injured tendons can present a considerable challenge, which considerably affects the motor function of limbs and leads to serious physical and mental pain, along with an economic burden on patients. Herein, we designed and fabricated a dipeptide hydrogel (DPH) using polypeptides P11-4 and P11-8. This hydrogel exhibited self-assembly characteristics and could be administered in vitro. To endow the hydrogel with differentiation and regeneration abilities, we added different concentrations of growth differentiation factor 5 (GDF5) to form GDF5@DPH. GDF5@DPH promoted the aggregation and differentiation of tendon stem/progenitor cells and promoted the regeneration and repair of tendon cells and collagen fibers in injured areas. In addition, GDF5@DPH inhibited inflammatory reactions in the injured area. Owing to its injectable properties, DPH can jointly inhibit adhesion and scar hyperplasia between tissues caused by endogenous inflammation and exogenous surgery and can provide a favorable internal environment for the regeneration and repair of the injured area. Overall, the GDF5@DPH system exhibits considerable promise as a novel approach to treating tendon injury.

Evidence has proved that intracranial aneurysm (IA) formation and rupture might be closely related to inflammatory response and oxidative stress. Our objective was to evaluate the potential of CD36 and glutathione (GSH) as biomarkers for IA. In this study, the enzyme-linked immunosorbent assay was used to measure the plasma levels of CD36 and GSH in 30 IA patients and 30 healthy controls. Then, correlation analysis, receiver operating characteristic (ROC) curve, and logistic regression analysis were performed. The results showed that the plasma level of CD36 in IA patients was significantly higher than that in the control group (P < 0.0001), and plasma GSH was significantly lower compared with that in the control group (P < 0.0001). ROC analysis showed that CD36 and GSH had high sensitivity (90.0 and 96.6%) and specificity (96.6 and 86.6%) for IA diagnosis. The combined sensitivity and specificity achieved were 100 and 100%, respectively. The plasma levels of CD36 and GSH did not show a significant correlation with age, the Glasgow Coma Scale, Hunter–Hess score, aneurysm size, aneurysm height, aneurysm neck, and aspect ratio. The AUC of the logistic regression model based on CD36 and GSH was 0.505. Our results suggested that the combination of plasma CD36 and GSH could serve as potential biomarkers for IA rupture.

Abstract Given afferent functions, sensory nerves have recently been found to exert efferent effects and directly alter organ physiology. Additionally, several studies have highlighted the indirect but crucial role of sensory nerves in the regulation of the physiological function of osteoclasts. Nonetheless, evidence regarding the direct sensory nerve efferent influence on osteoclasts is lacking. In the current study, we found that high levels of efferent signals were transported directly from the sensory nerves into osteoclasts. Furthermore, sensory hypersensitivity significantly increased osteoclastic bone resorption, and sensory neurons (SNs) directly promoted osteoclastogenesis in an in vitro coculture system. Moreover, we screened a novel neuropeptide, Cyp40, using an isobaric tag for relative and absolute quantitation (iTRAQ). We observed that Cyp40 is the efferent signal from sensory nerves, and it plays a critical role in osteoclastogenesis via the aryl hydrocarbon receptor (AhR)-Ras/Raf-p-Erk-NFATc1 pathway. These findings revealed a novel mechanism regarding the influence of sensory nerves on bone regulation, i.e., a direct promoting effect on osteoclastogenesis by the secretion of Cyp40. Therefore, inhibiting Cyp40 could serve as a strategy to improve bone quality in osteoporosis and promote bone repair after bone injury.

Abstract Background Single-cell RNA sequencing (scRNA-seq) measurements of gene expression show great promise for studying the cellular heterogeneity of rice roots. How precisely annotating cell identity is a major unresolved problem in plant scRNA-seq analysis due to the inherent high dimensionality and sparsity. Results To address this challenge, we present NRTPredictor, an ensemble-learning system, to predict rice root cell stage and mine biomarkers through complete model interpretability. The performance of NRTPredictor was evaluated using a test dataset, with 98.01% accuracy and 95.45% recall. With the power of interpretability provided by NRTPredictor, our model recognizes 110 marker genes partially involved in phenylpropanoid biosynthesis. Expression patterns of rice root could be mapped by the above-mentioned candidate genes, showing the superiority of NRTPredictor. Integrated analysis of scRNA and bulk RNA-seq data revealed aberrant expression of Epidermis cell subpopulations in flooding, Pi, and salt stresses. Conclusion Taken together, our results demonstrate that NRTPredictor is a useful tool for automated prediction of rice root cell stage and provides a valuable resource for deciphering the rice root cellular heterogeneity and the molecular mechanisms of flooding, Pi, and salt stresses. Based on the proposed model, a free webserver has been established, which is available at https://www.cgris.net/nrtp .

Abstract Organoids, three-dimensional structures cultured in vitro, can recapitulate the microenvironment, complex architecture, and cellular functions of in vivo organs or tissues. In recent decades, liver organoids have been developed rapidly, and their applications in biomedicine, such as drug screening, disease modeling, and regenerative medicine, have been widely recognized. However, the lack of repeatability and consistency, including the lack of standardized culture conditions, has been a major obstacle to the development and clinical application of liver organoids. It is time-consuming for researchers to identify an appropriate medium component scheme, and the usage of some ingredients remains controversial. In this review, we summarized and compared different methods for liver organoid cultivation that have been published in recent years, focusing on controversial medium components and discussing their advantages and drawbacks. We aimed to provide an effective reference for the development and standardization of liver organoid cultivation.

Abstract Vascular smooth muscle cells (VSMCs) are the major contributor to vascular repair and remodeling, which showed high level of phenotypic plasticity. Abnormalities in VSMC plasticity can lead to multiple cardiovascular diseases, wherein alternative splicing plays important roles. However, alternative splicing variants in VSMC plasticity are not fully understood. Here we systematically characterized the long-read transcriptome and their dysregulation in human aortic smooth muscle cells (HASMCs) by employing the Oxford Nanopore Technologies long-read RNA sequencing in HASMCs that are separately treated with platelet-derived growth factor, transforming growth factor, and hsa-miR-221-3P transfection. Our analysis reveals frequent alternative splicing events and thousands of unannotated transcripts generated from alternative splicing. HASMCs treated with different factors exhibit distinct transcriptional reprogramming modulated by alternative splicing. We also found that unannotated transcripts produce different open reading frames compared to the annotated transcripts. Finally, we experimentally validated the unannotated transcript derived from gene CISD1, namely CISD1-u, which plays a role in the phenotypic switch of HASMCs. Our study characterizes the phenotypic modulation of HASMCs from an insight of long-read transcriptome, which would promote the understanding and the manipulation of HASMC plasticity in cardiovascular diseases.