Progress of single-cell RNA sequencing combined with spatial transcriptomics in tumour microenvironment and treatment of pancreatic cancer.

In recent years, single-cell analyses have revealed the heterogeneity of the tumour microenvironment (TME) at the genomic, transcriptomic, and proteomic levels, further improving our understanding of the mechanisms of tumour development. Single-cell RNA sequencing (scRNA-seq) technology allow analysis of the transcriptome at the single-cell level and have unprecedented potential for exploration of the characteristics involved in tumour development and progression. These techniques allow analysis of transcript sequences at higher resolution, thereby increasing our understanding of the diversity of cells found in the tumour microenvironment and how these cells interact in complex tumour tissue. Although scRNA-seq has emerged as an important tool for studying the tumour microenvironment in recent years, it cannot be used to analyse spatial information for cells. In this regard, spatial transcriptomics (ST) approaches allow researchers to understand the functions of individual cells in complex multicellular organisms by understanding their physical location in tissue sections. In particular, in related research on tumour heterogeneity, ST is an excellent complementary approach to scRNA-seq, constituting a new method for further exploration of tumour heterogeneity, and this approach can also provide unprecedented insight into the development of treatments for pancreatic cancer (PC). In this review, based on the methods of scRNA-seq and ST analyses, research progress on the tumour microenvironment and treatment of pancreatic cancer is further explained.

Transfer learning-based PET/CT three-dimensional convolutional neural network fusion of image and clinical information for prediction of EGFR mutation in lung adenocarcinoma.

BACKGROUND: To introduce a three-dimensional convolutional neural network (3D CNN) leveraging transfer learning for fusing PET/CT images and clinical data to predict EGFR mutation status in lung adenocarcinoma (LADC). METHODS: Retrospective data from 516 LADC patients, encompassing preoperative PET/CT images, clinical information, and EGFR mutation status, were divided into training (n = 404) and test sets (n = 112). Several deep learning models were developed utilizing transfer learning, involving CT-only and PET-only models. A dual-stream model fusing PET and CT and a three-stream transfer learning model (TS_TL) integrating clinical data were also developed. Image preprocessing includes semi-automatic segmentation, resampling, and image cropping. Considering the impact of class imbalance, the performance of the model was evaluated using ROC curves and AUC values. RESULTS: TS_TL model demonstrated promising performance in predicting the EGFR mutation status, with an AUC of 0.883 (95%CI = 0.849-0.917) in the training set and 0.730 (95%CI = 0.629-0.830) in the independent test set. Particularly in advanced LADC, the model achieved an AUC of 0.871 (95%CI = 0.823-0.919) in the training set and 0.760 (95%CI = 0.638-0.881) in the test set. The model identified distinct activation areas in solid or subsolid lesions associated with wild and mutant types. Additionally, the patterns captured by the model were significantly altered by effective tyrosine kinase inhibitors treatment, leading to notable changes in predicted mutation probabilities. CONCLUSION: PET/CT deep learning model can act as a tool for predicting EGFR mutation in LADC. Additionally, it offers clinicians insights for treatment decisions through evaluations both before and after treatment.

Quality analysis of steamed beef with black tea and the mechanism of action of main active ingredients of black tea on myofibrillar protein.

In this study, we analyzed the tea polyphenol composition, volatile flavor composition and storage stability of steamed beef with black tea. The molecular docking and dynamics were used to elucidate the interaction mechanism between the active components of black tea and myofibrillar proteins. The highest content of caffeine (CAF) was found in black tea steamed beef products, followed by catechin (C), epicatechin gallate (ECG), epicatechin gallate (EGCG) and theaflavins (TF). Steamed beef with black tea showed low ΔE* value, low TBARS value, low carbonyl content as well as high sulfhydryl content during storage. The addition of C, CAF, ECG, EGCG and TF enhanced the oxidative stability of myofibrillar protein. In this study, the effects of active components of black tea on the oxidative stability of myofibrillar protein and their interactions were determined, which could provide a reference for the application of black tea and its active components in meat products. At the same time, it can provide new ideas for the development of new meat products.

New descriptions of the larval and pupal stages of Orthocladiusnitidoscutellatus and Psectrocladiusnevalis from Xizang, China (Diptera, Chironomidae).

Background: Tibetan Plateau is one of the most typical areas of biodiversity in the world because of its unique environmental and regional units, which breed unique biological communities and concentrate on many unique and rare wild animals and plants. Research on Chironomidae in the Tibetan Plateau is relatively weak. At present, the identification of Chironomidae species mainly depends on male adults, while identification of larvae and pupae is relatively difficult and there is less research on them. New information: During the investigations of insect diversity in the Tibetan Plateau, larval and pupal stages of Orthocladiusnitidoscutellatus Lundström, 1915 and Psectrocladiusnevalis Akhrorov, 1977 were described and illustrated. Matching and identification of larval and pupal stages were based on DNA barcodes. Neighbour-joining trees were reconstructed, based on known Orthocladius and Psectrocladius COI DNA barcodes, respectively.

Chromosome-scale genome assemblies of Himalopsyche anomala and Eubasilissa splendida (Insecta: Trichoptera).

Trichoptera is one of the most evolutionarily successful aquatic insect lineages and is highly valued value in adaptive evolution research. This study presents the chromosome-level genome assemblies of Himalopsyche anomala and Eubasilissa splendida achieved using PacBio, Illumina, and Hi-C sequencing. For H. anomala and E. splendida, assembly sizes were 663.43 and 859.28 Mb, with scaffold N50 lengths of 28.44 and 31.17 Mb, respectively. In H. anomala and E. splendida, we anchored 24 and 29 pseudochromosomes, and identified 11,469 and 10,554 protein-coding genes, respectively. The high-quality genomes of H. anomala and E. splendida provide critical genomic resources for understanding the evolution and ecology of Trichoptera and performing comparative genomics analyses.

DDX56 promotes EMT and cancer stemness via MELK-FOXM1 axis in hepatocellular carcinoma.

Hepatocellular carcinoma (HCC) is a major global cause of death, with epithelial-mesenchymal transition (EMT) and cancer stem cell (CSC)-like properties contributing to its metastasis. DEAD box helicase 56 (DDX56) is involved in carcinogenesis, but its role in EMT induction and stem phenotype maintenance is unclear. This study assessed the impact of DDX56 absence on HCC cell stemness and EMT. DDX56 was found to be overexpressed in HCC tissues, correlating with disease stage and prognosis. In vitro, DDX56 stimulated tumor cell proliferation, migration, invasion, EMT, and stemness. It also enhanced maternal embryonic leucine-zipper kinase (MELK)-mediated forkhead box protein M1 (FOXM1) expression, regulating cancer stemness and malignant traits. In vivo, DDX56 knockdown in tumor-bearing mice reduced tumorigenicity and lung metastasis by modulating the MELK-FOXM1 signaling pathway. Collectively, DDX56 initiates stem cell-like traits in HCC and promotes EMT via MELK-FOXM1 activation, shedding light on HCC pathogenesis and suggesting a potential anti-cancer therapeutic target.

Reducing the allergenicity of tropomyosin in shrimp by covalent conjugation with quercetin and chlorogenic acid.

The study aimed to assay the allergenicity of shrimp tropomyosin (TM) following covalent conjugation with quercetin (QR) and chlorogenic acid (CA). The structure of the TM-polyphenol covalent conjugates was examined by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE), circular dichroism (CD), fluorescence, differential scanning calorimetry (DSC), and Fourier Transform infrared spectroscopy (FTIR). Potential allergenicity was evaluated using in vitro and in vivo methods. The results showed that QR and CA induced structural changes in TM through aggregation. RBL-2H3 cell results showed that TM-QR and TM-CA covalent conjugates reduced the release of ß-hexosaminidase and histamine, respectively. In the mice model, TM-QR and TM-CA covalent conjugates reduced the level of IgE, IgG, IgG1, histamine, and mMCP-1 in sera. Furthermore, the allergenicity was reduced by suppressing Th2-related cytokines (IL-4, IL-5, IL-13) and promoting Th1-related cytokines (IFN-γ). These research findings demonstrate that the covalent binding of TM with QR and CA, modifies the allergenic epitopes of shrimp TM, thereby reducing its potential allergenicity. This approach holds practical applications in the production of low-allergenicity food within the food industry.

Deciphering morphology patterns of environmental microfibers: Insights into source apportionment.

Microfibers, a prevalent form of microplastics, undergo diverse environmental interactions resulting in varied morphological changes. These changes can offer insights into their environmental trajectories. Despite its importance, comprehensive studies on microfiber morphology are scarce. This study collected 233 microfibers from the East China Sea and South China Sea. Based on morphological features observed in microscopic images of microfibers, such as curvature, cross-sectional shapes, diameter variations, and crack shapes, we identified a general morphological pattern, classifying the environmental microfibers into three distinct morphological types. Our findings highlight noticeable differences in morphological metrics (e.g., length, diameter, and surface roughness) across three types, especially the diameter. Microfibers of Type I had an average diameter of 19.45 ± 4.93 µm, significantly smaller than Type II (263.00 ± 75.15 µm) and Type III (299.68 ± 85.62 µm). Within the three-dimensional (3D) space fully defined by these quantitative parameters, the clustering results of microfibers are also consistent with the proposed morphology pattern, with each category showing a potential correlation with specific chemical compositions. Type I microfibers correspond to synthetic cellulose, while 94.79 % of Types II and III are composed of polymers. Notably, we also validated the great applicability of the morphology categories to microfibers in diverse environmental compartments, including water and sediments in nearshore and offshore areas. This classification aids in the efficient determination of microfiber sources and the assessment of their ecological risks, marking a significant advancement in microfiber environmental studies.

Plasma metabolites as mediators in immune cell-pancreatic cancer risk: insights from Mendelian randomization.

Background: Immune cells play a crucial role in the development and progression of pancreatic cancer, yet the causal relationship remains uncertain due to complex immune microenvironments and conflicting research findings. Mendelian randomization (MR), this study aims to delineate the causal relationships between immune cells and pancreatic cancer while identifying intermediary factors. Methods: The genome-wide association study (GWAS) data on immune cells, pancreatic cancer, and plasma metabolites are derived from public databases. In this investigation, inverse variance weighting (IVW) as the primary analytical approach to investigate the causal relationship between exposure and outcome. Furthermore, this study incorporates MR-Egger, simple mode, weighted median, and weighted mode as supplementary analytical approaches. To ensure the reliability of our findings, we further assessed horizontal pleiotropy and heterogeneity and evaluated the stability of MR results using the Leave-one-out method. In conclusion, this study employed mediation analysis to elucidate the potential mediating effects of plasma metabolites. Results: Our investigation revealed a causal relationship between immune cells and pancreatic cancer, highlighting the pivotal roles of CD11c+ monocytes (odds ratio, ORIVW=1.105; 95% confidence interval, 95%CI: 1.002-1.218; P=0.045), HLA DR+ CD4+ antigen-presenting cells (ORIVW=0.920; 95%CI: 0.873-0.968; P=0.001), and HLA DR+ CD8br T cells (ORIVW=1.058; 95%CI: 1.002-1.117; P=0.041) in pancreatic cancer progression. Further mediation analysis indicated that oxalate (proportion of mediation effect in total effect: -11.6%, 95% CI: -89.7%, 66.6%) and the mannose to trans-4-hydroxyproline ratio (-19.4, 95% CI: -136%, 96.8%) partially mediate the relationship between HLA DR+ CD8br T cells and pancreatic cancer in nature. In addition, our analysis indicates that adrenate (-8.39%, 95% CI: -18.3%, 1.54%) plays a partial mediating role in the association between CD11c+ monocyte and pancreatic cancer, while cortisone (-26.6%, 95% CI: 138%, -84.8%) acts as a partial mediator between HLA DR+ CD4+ AC and pancreatic cancer. Conclusion: This MR investigation provides evidence supporting the causal relationship between immune cell and pancreatic cancer, with plasma metabolites serving as mediators. Identifying immune cell phenotypes with potential causal effects on pancreatic cancer sheds light on its underlying mechanisms and suggests novel therapeutic targets.

Genome-wide annotation and comparative analysis revealed conserved cuticular protein evolution among non-biting midges with varied environmental adaptability.

Chironomidae, non-biting midges, a diverse and abundant insect group in global aquatic ecosystems, represent an exceptional model for investigating genetic adaptability mechanisms in aquatic insects due to their extensive species diversity and resilience to various environmental conditions. The cuticle in insects acts as the primary defense against ecological pressures. Cuticular Proteins (CPs) determine cuticle characteristics, facilitating adaptation to diverse challenges. However, systematic annotation of CP genes has only been conducted for one Chironomidae species, Propsilocerus akamusi, by our team. In this study, we expanded this annotation by identifying CP genes in eight additional Chironomidae species, covering all Chironomidae species with available genome data. We identified a total of 889 CP genes, neatly categorized into nine CP families: 215 CPR RR1 genes, 272 CPR RR2 genes, 23 CPR RR3 genes, 21 CPF genes, 16 CPLCA genes, 19 CPLCG genes, 28 CPLCP genes, 77 CPAP genes, and 37 Tweedle genes. Subsequently, we conducted a comprehensive phylogenetic analysis of CPs within the Chironomidae family. This expanded annotation of CP genes across diverse Chironomidae species significantly contributes to our understanding of their remarkable adaptability.

Unveiling microplastic distribution and interactions in the benthic layer of the Yangtze River Estuary and East China Sea.

Microplastics (MPs), recognized as an emerging global environmental concern, have been extensively detected worldwide, with specific attention directed towards the Yangtze River Estuary (YRE) and East China Sea (ECS) regions. Despite their critical research significance, there remains a knowledge gap concerning the distribution of MPs in the benthic layer within this area, particularly regarding interactions governing their occurrence. Here we illuminate the distribution of MPs within the benthic layer and unravel the intricate interplay between bottom water and sediment in the YRE and ECS. We find that MPs are notably more abundant in bottom water, ranging from 8 to 175 times higher than in surface water. These MPs predominantly consist of polyester fibers, exhibit a size range between 0.5 and 5.0 mm, and display distinct coloration. Co-occurrence network analysis and Principal Coordinate Analysis confirm a robust correlation between MPs in bottom water and sediment, signifying the pivotal role of bottom water in mediating the distribution and transportation of MPs within the benthic layer. Furthermore, a positive correlation between MPs in sediment and bottom water turbidity underscores the impact of surface sediment resuspension and upwelling on MPs distribution. This study clarifies the intricate interactions within the benthic layer and highlights the crucial role of bottom water as a mediator in the vertical distribution of MPs, advancing our understanding of the "source-to-sink" transport processes governing MPs within water-sediment systems.

Chrysanthemum morifolium Ramat extract and probiotics combination ameliorates metabolic disorders through regulating gut microbiota and PPARα subcellular localization.

BACKGROUND: Chrysanthemum morifolium Ramat, a traditional Chinese medicine, has the effects on liver clearing, vision improving, and anti-inflammation. C. morifolium and probiotics have been individually studied for their beneficial effects on metabolic diseases. However, the underlying molecular mechanisms were not completely elucidated. This study aims to elucidate the potential molecular mechanisms of C. morifolium and probiotics combination (CP) on alleviating nonalcoholic fatty liver disease (NAFLD) and the dysregulation of glucose metabolism in high-fat diet (HFD)-fed mice. METHODS: The therapeutic effect of CP on metabolism was evaluated by liver histology and serum biochemical analysis, as well as glucose tolerance test. The impact of CP on gut microbiota was analyzed by 16S rRNA sequencing and fecal microbiota transplantation. Hepatic transcriptomic analysis was performed with the key genes and proteins validated by RT-qPCR and western blotting. In addition, whole body Pparα knockout (Pparα-/-) mice were used to confirm the CP-mediated pathway. RESULTS: CP supplementation ameliorated metabolic disorders by reducing body weight and hepatic steatosis, and improving glucose intolerance and insulin resistance in HFD fed mice. CP intervention mitigated the HFD-induced gut microbiota dysbiosis, which contributed at least in part, to the beneficial effect of improving glucose metabolism. In addition, hepatic transcriptomic analysis showed that CP modulated the expression of genes associated with lipid metabolism. CP downregulated the mRNA level of lipid droplet-binding proteins, such as Cidea and Cidec in the liver, leading to more substrates for fatty acid oxidation (FAO). Meanwhile, the expression of CPT1α, the rate-limiting enzyme of FAO, was significantly increased upon CP treatment. Mechanistically, though CP didn't affect the total PPARα level, it promoted the nuclear localization of PPARα, which contributed to the reduced expression of Cidea and Cidec, and increased expression of CPT1α, leading to activated FAO. Moreover, whole body PPARα deficiency abolished the anti-NAFLD effect of CP, suggesting the importance of PPARα in CP-mediated beneficial effect. CONCLUSION: This study revealed the hypoglycemic and hepatoprotective effect of CP by regulating gut microbiota composition and PPARα subcellular localization, highlighting its potential for therapeutic candidate for metabolic disorders.

Extracellular vesicles from normal tissues orchestrate the homeostasis of macrophages and attenuate inflammatory injury of sepsis.

Extracellular vesicles (EVs) exist throughout our bodies. We recently revealed the important role of intracardiac EVs induced by myocardial ischemia/reperfusion on cardiac injury and dysfunction. However, the role of EVs isolated from normal tissues remains unclear. Here we found that EVs, derived from murine heart, lung, liver and kidney have similar effects on macrophages and regulate the inflammation, chemotaxis, and phagocytosis of macrophages. Interestingly, EV-treated macrophages showed LPS resistance with reduced expressions of inflammatory cytokines and enhanced phagocytic activity. Furthermore, we demonstrated that the protein content in EVs contributed to the activation of inflammation, while the RNA component mainly limited the excessive inflammatory response of macrophages to LPS. The enrichment of miRNAs, including miR-148a-3p, miR-1a-3p and miR-143-3p was confirmed in tissue EVs. These EV-enriched miRNAs contributed to the inflammation remission in LPS induced macrophages through multiple pathways, including STAT3, P65 and SAPK/JNK. Moreover, administration of both EVs and EV-educated macrophages attenuated septic injury and cytokine storm in murine CLP models. Taken together, the present study disclosed that EVs from normal tissues can orchestrate the homeostasis of macrophages and attenuate inflammatory injury of sepsis. Therefore, tissue derived EVs or their derivatives may serve as potential therapeutic strategies in inflammatory diseases.