Браузер не даёт сохранять данные (например, приватный режим): закладки пропадут после закрытия вкладки.
Поиск статей PubMed
Ключевые слова, автор, журнал, годы — результаты из PubMed, аннотации с переводом на русский, закладки в браузере.
Найдено: 4 934
Страница 247 из 494-
Single-cell RNA-sequencing atlas reveals an FABP1-dependent immunosuppressive environment in hepatocellular carcinoma.
BACKGROUND: Single-cell RNA sequencing, also known as scRNA-seq, is a method profiling cell populations on an individual cell basis. It is particularly useful for more deeply understanding cell behavior in a complicated tumor microenvironment. Although several previous studies have examined scRNA-seq for hepatocellular carcinoma (HCC) tissues, no one has tested and analyzed HCC with different stages. METHODS: In this investigation, immune cells isolated from surrounding normal tissues and cancer tissues from 3 II-stage and 4 III-stage HCC cases were subjected to deep scRNA-seq. The analysis included 15 samples. We distinguished developmentally relevant trajectories, unique immune cell subtypes, and enriched pathways regarding differential genes. Western blot and co-immunoprecipitation were performed to demonstrate the interaction between fatty acid binding protein 1 (FABP1) and peroxisome proliferator-activated receptor gamma(PPARG). In vivo experiments were performed in a C57BL/6 mouse model of HCC established via subcutaneous injection. RESULTS: FABP1 was discovered to be overexpressed in tumor-associated macrophages (TAMs) with III-stage HCC tissues compared with II-stage HCC tissues. This finding was fully supported by immunofluorescence detection in significant amounts of HCC human samples. FABP1 deficiency in TAMs inhibited HCC progression in vitro. Mechanistically, FABP1 interacted with PPARG/CD36 in TAMs to increase fatty acid oxidation in HCC. When compared with C57BL/6 mice of the wild type, tumors in FABP1-/- mice consistently showed attenuation. The FABP1-/- group's relative proportion of regulatory T cells and natural killer cells showed a downward trend, while dendritic cells, M1 macrophages, and B cells showed an upward trend, according to the results of mass cytometry. In further clinical translation, we found that orlistat significantly inhibited FABP1 activity, while the combination of anti-programmed cell death 1(PD-1) could synergistically treat HCC progression. Liposomes loaded with orlistat and connected with IR780 probe could further enhance the therapeutic effect of orlistat and visualize drug metabolism in vivo. CONCLUSIONS: ScRNA-seq atlas revealed an FABP1-dependent immunosuppressive environment in HCC. Orlistat significantly inhibited FABP1 activity, while the combination of anti-PD-1 could synergistically treat HCC progression. This study identified new treatment targets and strategies for HCC progression, contributing to patients with advanced HCC from new perspectives.
-
Integrated single-cell and bulk RNA sequencing reveals prognostic and immunotherapy-associated myofibroblastic cancer-associated fibroblast subtypes in head and neck squamous cell carcinoma.
BACKGROUND: Cancer-associated fibroblasts (CAFs) are involved in some critical aspects of the pathogenesis of head and neck squamous cell carcinoma (HNSCC), including the formation of a tumor-permissive extracellular matrix (ECM) structure, angiogenesis, and the immune and metabolic reprogramming of the tumor microenvironment (TME). This study aimed to examine the plasticity and metabolic heterogeneity of CAFs in HNSCC patients before and after immunotherapy. METHODS: An integrated single-cell and bulk RNA sequencing (RNA-seq) analysis based on data from the GSE195832, GSE65868, and The Cancer Genome Atlas (TCGA)-HNSCC datasets was conducted. The functional plasticity and transcriptome diversity of the categorized CAF subtypes were analyzed using the DoRothEA tool and scMetabolism package. The relationship between the genes specifically expressed in the myofibroblast-like cancer-associated fibroblast (myCAF) subtype and prognosis was then examined by univariate and multivariate analyses. The influence of myCAF on immune cell modulation within the TME was analyzed using the Seurat and clusterProfiler packages. The therapeutic strategies for HNSCC were explored using the Cancer Therapeutics Response Portal (CTRP) and PRISM Repurposing datasets. RESULTS: In total, seven types of cells were annotated based on 11 clusters. The CAFs were then re-categorized into the following three subtypes: inflammatory cancer-associated fibroblasts (iCAFs), proliferating cancer-associated fibroblasts (pCAFs), and myCAFs. The percentage of myCAFs was reduced in HNSCC following the immunotherapy. The functional plasticity of the CAFs was further confirmed by the diverse enriched pathways. Notably, the myCAFs were closely associated with DNA repair, oxidative phosphorylation, and transcription factor E2F targets. Further, the myCAFs were found to be the subtype most relevant to the prognosis of HNSCC and were found to be involved in modulating the immune cells in the TME of HNSCC. Additionally, a higher myCAF score was related to the higher half-maximal inhibitory concentration (IC50) values of D-4476, GW-583340, spautin-1, and VER-155008, and the lower IC50 values of JTE-607, TG100-115, ML320, and TGX-221. Moreover, patients with lower myCAF scores responded better to immunotherapy. CONCLUSIONS: This study, which was based on single-cell and bulk RNA-seq analyses, showed the plasticity and metabolic heterogeneity of CAFs in HNSCC. Our findings may contribute to understandings of the immunotherapy response in HNSCC.
-
The neurotoxicity of Chlorantraniliprole to Helicoverpa armigera larvae.
Chlorantraniliprole (CAP) is a mainstream diamide insecticide widely used against lepidopteran pests such as Helicoverpa armigera. Given that most insecticides act via neurotoxic mechanisms, we reasoned that CAP, despite its well-established action on ryanodine receptors (RyRs), may also disrupt nervous system function through additional targets. Insect neurotoxicity is a coordinated process involving neurons and glial cells: voltage-gated sodium (Nav) and potassium (Kv) channels are common insecticide targets, however, their involvement in CAP-induced neurotoxicity has not been established, and glial contributions are poorly understood. We elucidated CAP's multi-target mechanisms by constructing the first single-cell transcriptomic atlas of the H. armigera ventral nerve cord (VNC) using scRNA-seq, validated by whole-cell patch-clamp electrophysiology and RT-qPCR. Results showed that CAP modulated the kinetics of Nav channel in a concentration-dependent manner and suppressed Kv channel currents, confirming both as novel non-canonical targets. scRNA-seq identified VNC cell types, identifying NKCC (perineurial glia-enriched) and UGT39B1 (subperineurial glia-enriched); both were upregulated after 24 h LC30 CAP exposure. These results indicate that CAP modulates Nav and Kv channels at relatively high concentrations. As potential functional targets, these channels supplement the primary RyR-mediated action of CAP, and imply a partial mechanistic similarity to pyrethroids via regulation of Nav channels. Moreover, the VNC atlas facilitated the identification of glial-specific markers (NKCC and UGT39B1), clarifying glial involvement. Collectively, our work advances multi-target understanding of diamide insecticides, provides candidate synergists, and supports "neuron-glial dual-target" strategies for managing H. armigera resistance.
-
PRDM1 Drives a TIM3+ Macrophage Immunosuppressive Niche via LGALS9 Signaling in Prostate Cancer Progression.
Background: Prostate cancer (PCa) responds poorly to immunotherapy. We investigated the myeloid checkpoint TIM3 (HAVCR2) to define its lineage localization and regulatory logic in the PCa microenvironment. Methods: We integrated stage-resolved public single-cell RNA-seq datasets spanning primary PCa, metastatic hormone-sensitive PCa, and castration-resistant PCa. Myeloid compartments were analyzed via differential expression, regulon inference, and ligand-receptor modeling. Clinical relevance was evaluated in the Cancer Genome Atlas prostate adenocarcinoma (TCGA-PRAD) cohort and independent cohorts using a myeloid TIM3 signature. Mechanistic validation was achieved through PR domain zinc finger protein 1 (PRDM1) chromatin immunoprecipitation followed by Chromatin Immunoprecipitation (ChIP)-qPCR (ChIP-qPCR), TIM3-promoter luciferase assays, and functional perturbation of the galectin 9 (LGALS9)-TIM3 signaling pathway in macrophages differentiated. Results: TIM3 expression was predominantly confined to monocytes/macrophages, indicating TIM3 as a microenvironmental checkpoint in PCa. TIM3_high macrophages formed a Secreted Phosphoprotein 1 (SPP1)-enriched tumor-associated macrophage (TAM) state coupled to chemokine programs and extracellular matrix remodeling. Regulon profiling nominated PR domain zinc finger protein 1 (PRDM1) as an upstream driver; PRDM1 correlated with TIM3. Communication inference further highlighted an LGALS9-TIM3 axis and a C-X-C motif chemokine receptor 4/integrin subunit beta 1 (CXCR4/ITGB1)-associated permissive niche. Recombinant LGALS9 induced TIM3-linked M2-like macrophages polarization and increased CXCR4/ITGB1, which was attenuated by TIM3 blockade. Conclusions: Our results delineate a PRDM1-licensed TIM3_high macrophage program sustained by an LGALS9-TIM3 reinforcement loop and coupled to immunosuppressive and remodeling-associated phenotypes. Targeting TIM3 in the myeloid compartment, alone or in rational combinations, may represent a feasible strategy to reprogram tumor-associated macrophage states in PCa.
-
Multimodal evidence for bone lymphatics in skeletal health and repair.
Previous studies predominantly associated lymphatics with skeletal disease and bone loss. However, building on our work, bone lymphatics are emerging as a paradigm-shifting component of the skeletal microenvironment, illustrating their role as positive regulators of bone mass and repair. Here, we present a comprehensive analysis integrating spatial transcriptomics, single-cell RNA sequencing, and imaging across murine and human bones. Spatial transcriptomics identifies Prox1+ endothelial cells embedded within bone. Reanalysis of multiple scRNA-seq datasets confirms Prox1+ lymphatic endothelial cells (LECs) in bones, despite their underrepresentation in soft-tissue endothelial cell atlases. Periosteum is an insufficient source for bone lymphatics because it contains only sparse LECs. Our analyses further demonstrate that certain mouse models lack the sensitivity required to detect bone lymphatics and highlight the importance of high-resolution imaging. Collectively, convergent multimodal evidence substantiates LECs as an integral functional component of the skeletal microenvironment. This Matters Arising Response paper addresses the Meng et al. (2026) Matters Arising paper, published concurrently in this issue.
-
In silico analysis of inner ear development using public whole embryonic body single-cell RNA-sequencing data.
The inner ear comprises four epithelial domains: the cochlea, vestibule, semicircular canals, and endolymphatic duct/sac. These structures are segregated at embryonic day 13.5 (E13.5). However, these four anatomical structures remain undefined at E10.5. Here, we aimed to identify lineage-specific genes in the early developing inner ear using published data obtained from single-cell RNA-sequencing (scRNA-seq) of embryonic mice. We downloaded 5000 single-cell transcriptome data, named 'auditory epithelial trajectory', from the Mouse Organogenesis Cell Atlas. The dataset was supposed to include otic epithelial cells at E9.5-13.5. We projected the 5000 cells onto a two-dimensional space encoding the transcriptional state and visualised the pattern of otic epithelial cell differentiation. We identified 15 clusters, which were annotated as one of the four components of the inner ear epithelium using known genes that characterise the four different tissues. Additionally, we classified 15 clusters into sub-regions of the four inner ear components. By comparing transcriptomes between these 15 clusters, we identified several candidates of lineage-specific genes. Characterising these new candidate genes will help future studies about inner ear development.
-
Integrated Analysis of Single-Cell and Bulk RNA-Sequencing Based on EcoTyper Machine Learning Framework Identifies Cell-State-Specific M2 Macrophage Markers Associated with Gastric Cancer Prognosis.
BACKGROUND: Tumor is a complex and dynamic ecosystem formed by the interaction of numerous diverse cells types and the microenvironments they inhabit. Determining how cellular states change and develop distinct cellular communities in response to the tumor microenvironment is critical to understanding cancer progression. Tumour-associated macrophages (TAMs) are an important component of the tumour microenvironment and play a crucial role in cancer progression. This study was designed to identify cell-state-specific M2 macrophage markers associated with gastric cancer (GC) prognosis through integrative analysis of single-cell RNA sequencing (scRNA-seq) and bulk RNA-seq data using a machine learning framework named EcoTyper. RESULTS: The results showed that TAMs were classified into M1 macrophages, M2 macrophages, monocytes, undefined macrophages and dendritic cells, with M2 macrophages predominating. EcoTyper assigned macrophages to different cell states and ecotypes. A total of 168 cell-state-specific M2 macrophage markers were obtained by integrative analysis of scRNA-seq and bulk RNA-seq data. These markers could categorize GC patients into two clusters (clusters A and B) with different survival and M2 macrophages infiltration abundance. Cell adhesion molecules, cytokine-cytokine receptor interaction, JAK/STAT pathway, MAPK pathway were significantly enriched in cluster A, which had worse survival and higher M2 macrophages infiltration. CONCLUSION: In conclusion, this study profiles a single-cell atlas of intratumor heterogeneity and defines the cell states and ecotypes of TAMs in GC. Furthermore, we have identified prognostically relevant cell-state-specific M2 macrophage markers. These findings provide novel insights into the tumor ecosystem and cancer progression.
-
Integrated Single-Nucleus Multi-Omics Atlases Reveal Lineage Plasticity and Regulatory Networks of Luminal Epithelial Cells During Mammary Gland Lactation and Involution.
Dynamic changes in mammary cells are essential for sustaining lactation and maintaining epithelial homeostasis. However, the phenotypic transition process of mammary cells during lactation remains unclear. Here, single-nucleus RNA sequencing (snRNA-seq) of 64 199 cells and single-nucleus chromatin accessibility sequencing (snATAC-seq) of 78 984 cells were generated from the goat mammary gland of dry and lactation stages. A total of 18 cell types were annotated, and spatial transcriptomic analysis confirmed the localization of lactation-related cell types within the mammary tissue. Enrichment analysis of SNP within cell type-specific chromatin accessibility regions revealed strong associations between mammary epithelial cells (MECs) with milk production traits. To further explore the MECs functional diversification during lactation and their differences from the dry stage, four differentiation trajectories from luminal progenitor to luminal mature cells were reconstructed. Lineage-specific gene regulatory networks (GRNs) were constructed by integrating snRNA-seq and snATAC-seq data, and stage-specific signals were identified through cell-cell communications. Finally, to explore the evolutionary conservation and divergence of MECs, cross-species comparative analyses were conducted and revealed MEC differential evolutionary rates, conserved milk-producing subtypes, and lineage-specific populations driving species-specific differences in milk composition. Overall, these findings uncover the coordinated transcriptional and chromatin dynamics that drive mammary epithelial differentiation and functional maintenance during lactation.
-
Automatic quality control of single-cell and single-nucleus RNA-seq using valiDrops.
Single-cell and single-nucleus RNA-sequencing (sxRNA-seq) measures gene expression in individual cells or nuclei enabling comprehensive characterization of cell types and states. However, isolation of cells or nuclei for sxRNA-seq releases contaminating RNA, which can distort biological signals, through, for example, cell damage and transcript leakage. Thus, identifying barcodes containing high-quality cells or nuclei is a critical analytical step in the processing of sxRNA-seq data. Here, we present valiDrops, an automated method to identify high-quality barcodes and flag dead cells. In valiDrops, barcodes are initially filtered using data-adaptive thresholding on community-standard quality metrics, and subsequently, valiDrops uses a novel clustering-based approach to identify barcodes with distinct biological signals. We benchmark valiDrops and show that biological signals from cell types and states are more distinct, easier to separate and more consistent after filtering by valiDrops compared to existing tools. Finally, we show that valiDrops can predict and flag dead cells with high accuracy. This novel classifier can further improve data quality or be used to identify dead cells to interrogate the biology of cell death. Thus, valiDrops is an effective and easy-to-use method to improve data quality and biological interpretation. Our method is openly available as an R package at www.github.com/madsen-lab/valiDrops.
-
Single-nucleus RNA-Seq reveals apical-basal polarity as a somatic embryogenesis checkpoint in Picea abies.
Somatic embryogenesis is pivotal for conifer propagation, yet its molecular basis remains poorly understood in gymnosperms. Single-nucleus RNA-seq offers unprecedented resolution for deciphering cell-type-specific transcriptional dynamics during gymnosperm embryogenesis. Here, we constructed a high-resolution transcriptomic atlas of Norway spruce (Picea abies) using high-efficiency and non/low-efficiency proembryogenic masses (HEMs and LEMs) collected before and after somatic embryo induction. Analysis of 55,635 nuclei identified 11 clusters, including somatic embryogenic cells (SCs) responsible for somatic embryo formation. Developmental trajectory analysis revealed a polarity-associated state S6 enriched in SCs, which was abundant in HEMs but nearly absent in LEMs. Key polarity genes, such as ROP-Guanine Exchange Factors, a homolog of PIN-FORMED 1, and PaWOX2, were enriched in the S6 state. Strikingly, overexpression of P. abies AGAMOUS-like 104 (PaAGL104), an S6-enriched transcription factor, induced excessive suspensor growth and apical-basal defects in both HEMs and LEMs embryos. TUNEL assays showed impaired suspensor elimination via suppressed programmed cell death in PaAGL104 overexpressors. Spatial expression analysis using a PaAGL104pro::NLS-mCherry reporter line revealed dynamic expression from ubiquitous to basal-enriched in the embryo proper. This region potentially contains the htube cell", a gymnosperm-specific stem cell crucial for suspensor formation and embryonic polarization. Our study identifies embryonic polarization as a key developmental checkpoint in conifer somatic embryogenesis and provides a high-resolution transcriptomic atlas of gymnosperm callus. These findings advance our understanding of totipotency in spruce and offer practical insights for improving clonal propagation in forestry.