搜索结果: 'gmp t cell activator'

SummaryMotivated by the cellular heterogeneity in complex tissues,particularly in brain and induced pluripotent stem cell (iPSC)-derived brain models,we developed a complete workflow to reproducibly characterize cell types in complex tissues. Our approach combines a flow cytometry (FC) antibody panel with our computational pipeline CelltypeR,enabling dataset aligning,unsupervised clustering optimization,cell type annotating,and statistical comparisons. Applied to human iPSC derived midbrain organoids,it successfully identified the major brain cell types. We performed fluorescence-activated cell sorting of CelltypeR-defined astrocytes,radial glia,and neurons,exploring transcriptional states by single-cell RNA sequencing. Among the sorted neurons,we identified subgroups of dopamine neurons: one reminiscent of substantia nigra cells most vulnerable in Parkinson’s disease. Finally,we used our workflow to track cell types across a time course of organoid differentiation. Overall,our adaptable analysis framework provides a generalizable method for reproducibly identifying cell types across FC datasets in complex tissues. Graphical abstract Highlights•CelltypeR is a flow cytometry and computational pipeline for cell type quantification•Identified brain cell types in midbrain organoids and measured changes in proportions•Enriched selected populations using FACS and characterized by single-cell RNA sequencing•Identified substantia nigra–like dopaminergic neurons sensitive in Parkinson’s disease Neuroscience; Cell biology; Omics View Publication

The emergence of retinal progenitor cells and differentiation to various retinal cell types represent fundamental processes during retinal development. Herein,we provide a comprehensive single cell characterisation of transcriptional and chromatin accessibility changes that underline retinal progenitor cell specification and differentiation over the course of human retinal development up to midgestation. Our lineage trajectory data demonstrate the presence of early retinal progenitors,which transit to late,and further to transient neurogenic progenitors,that give rise to all the retinal neurons. Combining single cell RNA-Seq with spatial transcriptomics of early eye samples,we demonstrate the transient presence of early retinal progenitors in the ciliary margin zone with decreasing occurrence from 8 post-conception week of human development. In retinal progenitor cells,we identified a significant enrichment for transcriptional enhanced associate domain transcription factor binding motifs,which when inhibited led to loss of cycling progenitors and retinal identity in pluripotent stem cell derived organoids. Formation of the retina during development involves the coordinated action of retinal progenitor cells and their differentiated cell types,which is key for producing a functioning eye. Here the authors provide a detailed atlas of human retinal development,combining scRNA-seq and spatial transcriptomics,and identify key genetic factors that mediate retinal progenitor cell proliferation and differentiation. View Publication

SUMMARY Circular RNAs (circRNAs) are stable RNAs present in cell-free RNA,which may comprise cellular debris and pathogen genomes. Here we investigate the phenomenon and mechanism of cellular uptake and intracellular fate of exogenous circRNAs. Human myeloid cells and B cells selectively internalize extracellular circRNAs. Macrophage uptake of circRNA is rapid,energy-dependent,and saturable. CircRNA uptake can lead to translation of encoded sequences and antigen presentation. The route of internalization influences immune activation after circRNA uptake,with distinct gene expression programs depending on the route of RNA delivery. Genome-scale CRISPR screens and chemical inhibitor studies nominate macrophage scavenger receptor MSR1,toll-like receptors,and mTOR signaling as key regulators of receptor-mediated phagocytosis of circRNAs,a dominant pathway to internalize circRNAs in parallel to macropinocytosis. These results suggest that cell-free circRNA serves as an “eat me” signal and danger-associated molecular pattern,indicating orderly pathways of recognition and disposal. eTOC Blurb: Amaya et. al. explores how cells take up extracellular circular RNAs (CircRNAs) and their impact on immune signaling. Macrophages readily internalize circRNAs,and this study identifies the specific receptors and signaling pathways governing circRNA internalization,highlighting their role as signaling molecules for immune recognition and disposal. Graphical Abstract View Publication

Presepsin (P-SEP) is a specific biomarker for sepsis. Monocytes produce P-SEP by phagocytosing neutrophil extracellular traps (NETs). Herein,we investigated whether M1 macrophages (M1 MΦs) are the primary producers of P-SEP after NET phagocytosis. We co-cultured M1 MΦs and NETs from healthy participants,measured P-SEP levels in the culture medium supernatant,and detected P-SEP using western blotting. When NETs were co-cultured with M1 MΦs,the P-SEP level of the culture supernatant was high. Notably,we demonstrated,for the first time,the intracellular kinetics of P-SEP production by M1 MΦs via NET phagocytosis: M1 MΦs produced P-SEP intracellularly 15 min after NET phagocytosis and then released it extracellularly. In a sepsis mouse model,the blood NET ratio and P-SEP levels,detected using ELISA,were significantly increased (p < 0.0001). Intracellular P-SEP analysis via flow cytometry demonstrated that lung,liver,and kidney MΦs produced large amounts of P-SEP. Therefore,we identified these organs as the origin of M1 MΦs that produce P-SEP during sepsis. Our data indicate that the P-SEP level reflects the trend of NETs,suggesting that monitoring P-SEP can be used to both assess NET-induced organ damage in the lungs,liver,and kidneys during sepsis and determine treatment efficacy. View Publication

IntroductionChronic inflammation of the gastrointestinal tissues underlies gastrointestinal inflammatory disorders,leading to tissue damage and a constellation of painful and debilitating symptoms. These disorders include inflammatory bowel diseases (Crohn’s disease and ulcerative colitis),and eosinophilic disorders (eosinophilic esophagitis and eosinophilic duodenitis). Gastrointestinal inflammatory disorders can often present with overlapping symptoms necessitating the use of invasive procedures to give an accurate diagnosis.MethodsThis study used peripheral blood mononuclear cells from individuals with Crohn’s disease,ulcerative colitis,eosinophilic esophagitis,and eosinophilic duodenitis to better understand the alterations to the transcriptome of individuals with these diseases and identify potential markers of active inflammation within the peripheral blood of patients that may be useful in diagnosis. Single-cell RNA-sequencing was performed on peripheral blood mononuclear cells isolated from the blood samples of pediatric patients diagnosed with gastrointestinal disorders,including Crohn’s disease,ulcerative colitis,eosinophilic esophagitis,eosinophilic duodenitis,and controls with histologically healthy gastrointestinal tracts.ResultsWe identified 730 (FDR < 0.05) differentially expressed genes between individuals with gastrointestinal disorders and controls across eight immune cell types.DiscussionThere were common patterns among GI disorders,such as the widespread upregulation of MTRNR2L8 across cell types,and many differentially expressed genes showed distinct patterns of dysregulation among the different gastrointestinal diseases compared to controls,including upregulation of XIST across cell types among individuals with ulcerative colitis and upregulation of Th2-associated genes in eosinophilic disorders. These findings indicate both overlapping and distinct alterations to the transcriptome of individuals with gastrointestinal disorders compared to controls,which provide insight as to which genes may be useful as markers for disease in the peripheral blood of patients. View Publication

Background: The complex aetiology of type 1 diabetes (T1D),characterised by a detrimental cross-talk between the immune system and insulin-producing beta cells,has hindered the development of effective disease-modifying therapies. The discovery that the pharmacological activation of LRH-1/NR5A2 can reverse hyperglycaemia in mouse models of T1D by attenuating the autoimmune attack coupled to beta cell survival/regeneration prompted us to investigate whether immune tolerisation could be translated to individuals with T1D by LRH-1/NR5A2 activation and improve islet survival. Methods: Peripheral blood mononuclear cells (PBMCs) were isolated from individuals with and without T1D and derived into various immune cells,including macrophages and dendritic cells. Cell subpopulations were then treated or not with BL001,a pharmacological agonist of LRH-1/NR5A2,and processed for: (1) Cell surface marker profiling,(2) cytokine secretome profiling,(3) autologous T-cell proliferation,(4) RNAseq and (5) proteomic analysis. BL001-target gene expression levels were confirmed by quantitative PCR. Mitochondrial function was evaluated through the measurement of oxygen consumption rate using a Seahorse XF analyser. Co-cultures of PBMCs and iPSCs-derived islet organoids were performed to assess the impact of BL001 on beta cell viability. Results: LRH-1/NR5A2 activation induced a genetic and immunometabolic reprogramming of T1D immune cells,marked by reduced pro-inflammatory markers and cytokine secretion,along with enhanced mitohormesis in pro-inflammatory M1 macrophages and mitochondrial turnover in mature dendritic cells. These changes induced a shift from a pro-inflammatory to an anti-inflammatory/tolerogenic state,resulting in the inhibition of CD4+ and CD8+ T-cell proliferation. BL001 treatment also increased CD4+/CD25+/FoxP3+ regulatory T-cells and Th2 cells within PBMCs while decreasing CD8+ T-cell proliferation. Additionally,BL001 alleviated PBMC-induced apoptosis and maintained insulin expression in human iPSC-derived islet organoids. Conclusion: These findings demonstrate the potential of LRH-1/NR5A2 activation to modulate immune responses and support beta cell viability in T1D,suggesting a new therapeutic approach. Key points: LRH-1/NR5A2 activation in inflammatory cells of individuals with type 1 diabetes (T1D) reduces pro-inflammatory cell surface markers and cytokine release. LRH-1/NR5A2 promotes a mitohormesis-induced immuno-resistant phenotype to pro-inflammatory macrophages. Mature dendritic cells acquire a tolerogenic phenotype via LRH-1/NR5A2-stimulated mitochondria turnover. LRH-1/NR5A2 agonistic activation expands a CD4+/CD25+/FoxP3+ T-cell subpopulation. Pharmacological activation of LRH-1/NR5A2 improves the survival iPSC-islets-like organoids co-cultured with PBMCs from individuals with T1D. View Publication

BackgroundLung cancer,particularly non-small cell lung cancer (NSCLC),has high recurrence rates and remains a leading cause of cancer-related death,despite recent advances in its treatment. Emerging therapies,such as chimeric antigen receptor (CAR)-T cell therapy,have shown promise but face significant challenges in targeting solid tumors. This study investigated the potential of combining receptor tyrosine kinase-like orphan receptor 1 (ROR1)-targeting CAR-T cells with ferroptosis inducers to promote ferroptosis of tumor cells and enhance anti-tumor efficacy.MethodsRNA-seq data and immunofluorescence analysis of relapsed NSCLC patient samples were used to explore ROR1 expression. In addition,ROR1-targeting CAR-T cells were developed to assess cytotoxic activity against ROR1+ tumor cells,and the effect of cytokine stimulation on their efficacy was evaluated. Lipidomics,immunofluorescent histochemistry,and western blotting were used to explore the observed effects. Ferroptosis indicators,including levels of reactive oxygen species,were used to detect the combined effect of CAR-T cells and ferroptosis-inducing drugs. Finally,tumor-bearing mice were used to validate the in vivo efficacy of the combination therapy strategy.ResultsTumor cells treated with ferroptosis inducers showed increased sensitivity to Interferon gamma (IFN-γ) secreted by ROR1 CAR-T cells. Furthermore,ROR1 CAR-T cells enhanced the production of phosphatidylcholine with diacyl-polyunsaturated fatty acid tails (PC-PUFA2) by working in tandem with IFN-γ. This enhancement promoted the expression of acyl-CoA synthetase long chain family member 4 (ACSL4),which in turn strengthened the overall anti-tumor response.ConclusionsCombining ROR1 CAR-T cells with ferroptosis inducers enhanced anti-tumor efficacy in NSCLC by promoting ferroptosis through increased lipid peroxidation.Supplementary InformationThe online version contains supplementary material available at 10.1186/s40364-025-00730-0. View Publication

Background and aimsMortality rates for hepatocellular carcinoma (HCC) remain high,while multimodal treatment approaches offer new perspectives. Here,we investigated the association of extracellular nicotinamide adenine dinucleotide (eNAD+) on ecto-nucleotide pyrophosphatase/phosphodiesterase 1 (CD203a,ENPP1 or PC-1) on Th17 cells in relation to the likelihood of HCC recurrence following liver resection.MethodThe study compared heparinized blood plasma samples from 95 patients who underwent liver resection,including 25 patients with HCC and 24 control patients without liver disease. Plasma eNAD+ concentrations were determined using a heat-based dichotomous pH extraction method,followed by enzymatic cycling and a colorimetric assay for quantification. Fibrosis was graded histologically using the Desmet score (F0–F4). Surface expression analysis was performed using flow cytometry.ResultsWith increasing grades of liver fibrosis predominant in HCC patients,a significant reduction in plasma eNAD+ concentrations was measured (p < 0.05). Further,a significant correlation was found between HCC patients and CD203a expression on CD4+,CCR4+ as well as CCR6+ T cells (p < 0.05). Patients who exhibited high proportions of CD203a expressing Th17 cells (CD4+,CCR6+ CCR4+) post surgery were found to be at a sixfold increased risk (HR 6.38,95% Cl 1.51–27.00) of HCC recurrence and had a median recurrence-free survival of 233 days (p < 0.05),compared to patients with low CD203a expressing Th17 cells (CD4+ CCR6+ CCR4+). Similarly,patients who had a high proportion of CD203a expressing Th17 cells (CD4+ CCR6+) following surgery had a fivefold increased risk (HR 5.56,95% Cl 1.58–19.59) of HCC recurrence and a median recurrence-free survival of 334 days (p < 0.05) compared to those with low CD203a expressing Th17 cells (CCR6+).ConclusionThe data indicates that eNAD+ levels are decreased in patients with liver fibrosis or cirrhosis. Strikingly,patients with high CD203a expression on Th17 cells had a significantly increased likelihood of recurrence,highlighting its potential as a valuable prognostic marker and a possible therapeutic target.Supplementary InformationThe online version contains supplementary material available at 10.1007/s00432-025-06155-4. View Publication

AbstractImmunodeficient mouse models are widely used for the assessment of human normal and leukemic stem cells. Despite the advancements over the years,reproducibility,as well as the differences in the engraftment of human cells in recipient mice remains to be fully resolved. Here,we used various immunodeficient mouse models to characterize the effect of donor–recipient sex on the engraftment of the human leukemic and healthy cells. Donor human cells and recipient immunodeficient mice demonstrate sex‐specific engraftment levels with significant differences observed in the lineage output of normal CD34+ hematopoietic stem and progenitor cells upon xenotransplantation. Intriguingly,human female donor cells display heightened sensitivity to the recipient mice's gender,influencing their proliferation and resulting in significantly increased engraftment in female recipient mice. Our study underscores the intricate interplay taking place between donor and recipient characteristics,shedding light on important considerations for future studies,particularly in the context of pre‐clinical research. View Publication

Segmentation is required to quantify cellular structures in microscopic images. This typically requires their fluorescent labeling. Convolutional neural networks (CNNs) can detect these structures also in only transmitted light images. This eliminates the need for transgenic or dye fluorescent labeling,frees up imaging channels,reduces phototoxicity and speeds up imaging. However,this approach currently requires optimized experimental conditions and computational specialists. Here,we introduce “aiSEGcell” a user-friendly CNN-based software to segment nuclei and cells in bright field images. We extensively evaluated it for nucleus segmentation in different primary cell types in 2D cultures from different imaging modalities in hand-curated published and novel imaging data sets. We provide this curated ground-truth data with 1.1 million nuclei in 20,000 images. aiSEGcell accurately segments nuclei from even challenging bright field images,very similar to manual segmentation. It retains biologically relevant information,e.g. for demanding quantification of noisy biosensors reporting signaling pathway activity dynamics. aiSEGcell is readily adaptable to new use cases with only 32 images required for retraining. aiSEGcell is accessible through both a command line,and a napari graphical user interface. It is agnostic to computational environments and does not require user expert coding experience. Author summaryFluorescence microscopy is the most widely used method to monitor cellular structures in space and time. Fluorescently labeling cellular structures is typically required to localize (“segment”) them in electronic images for subsequent quantification. Deep learning approaches can detect these structures also in only bright field images. This eliminates the need for a fluorescent label,frees up imaging channels,speeds up imaging,and reduces the harmful effects of exposing cells to high intensity light. However,label free segmentation currently requires optimized experimental conditions and computational specialists. Therefore,we developed “aiSEGcell” a user-friendly deep learning-based software to segment nuclei and cells in only bright field images. We extensively evaluated aiSEGcell on different common experimental conditions and showed that biologically even sensitive relevant information is retained. Furthermore,we demonstrated that aiSEGcell is adaptable by retraining to new applications with very little required data. We make it accessible for users with no required expert coding experience in a wide range of computational environments. Finally,we openly share our very large imaging data sets to further the development of other segmentation approaches. View Publication

Durable response to chimeric antigen receptor T (CART) cell therapy remains limited in part due to CART cell exhaustion. Here,we investigate the regulation of CART cell exhaustion with three independent approaches including: a genome-wide CRISPR knockout screen using an in vitro model for exhaustion,RNA and ATAC sequencing on baseline and exhausted CART cells,and RNA and ATAC sequencing on pre-infusion CART cell products from responders and non-responders in the ZUMA-1 clinical trial. Each of these approaches identify interleukin (IL)-4 as a regulator of CART cell dysfunction. Further,IL-4-treated CD8+ CART cells develop signs of exhaustion independently of the presence of CD4+ CART cells. Conversely,IL-4 pathway editing or the combination of CART cells with an IL-4 monoclonal antibody improves antitumor efficacy and reduces signs of CART cell exhaustion in mantle cell lymphoma xenograft mouse models. Therefore,we identify both a role for IL-4 in inducing CART exhaustion and translatable approaches to improve CART cell therapy. The application and therapeutic success of CAR-T cell approaches are limited by the development of T cell exhaustion. Here,Stewart et al discover a role for IL-4 in driving CD8+ CAR-T cell exhaustion and demonstrate the improvement of CAR-T cell effectivity with interruption of IL-4 signalling. View Publication

Inflammatory bowel disease (IBD),encompassing Crohn’s disease (CD) and ulcerative colitis (UC),is a chronic inflammatory condition of the gut affecting both adults and children. Neutrophil extracellular traps (NETs) are structures released by activated neutrophils,potentially contributing to tissue damage in various diseases. This study aimed to explore the presence and role of NETs in pediatric IBD. We compared intestinal biopsies and peripheral blood from 20 pediatric IBD patients (UC and CD) to controls. Biopsy staining and techniques for neutrophil activation were used to assess neutrophil infiltration and NET formation. We also measured the enzymatic activity of key NET proteins and evaluated NET formation in UC patients in remission. Both UC and CD biopsies showed significantly higher levels of neutrophils and NETs compared to controls (p < 0.01),with UC exhibiting the strongest association. Peripheral blood neutrophils from UC patients at diagnosis displayed increased NET formation compared to controls and CD patients. Interestingly,NET formation normalized in UC patients following remission-inducing treatment. This pilot study suggests a potential role for NETs in pediatric IBD,particularly UC. These findings warrant further investigation into the mechanisms of NET involvement and the potential for targeting NET formation as a therapeutic strategy. View Publication