Blood and immune cell engineering: Cytoskeletal contractility and nuclear rheology impact cell lineage and localization

AbstractCell-based immunotherapies have tremendous potential to treat many diseases, such as activating immunity in cancer or suppressing it in autoimmune diseases. Most cell-based cancer immunotherapies in the clinic provide adjuvant signals through genetic engineering to enhance T cell functions. However, genetically encoded signals have minimal control over dosing and persist for the life of a cell lineage. These properties make it difficult to balance increasing therapeutic efficacy with reducing toxicities. Here, we demonstrated the potential of phospholipid-coupled ligands as a non-genetic system for immune cell engineering. This system provides simple, controlled, non-genetic adjuvant delivery to immune cells via lipid-mediated insertion into plasma membranes. Lipid-mediated insertion (depoting) successfully delivered Toll-like receptor (TLR) ligands intracellularly and onto cell surfaces of diverse immune cells. These ligands depoted into immune cells in a dose-controlled fashion and did not compete during multiplex pairwise loading. Immune cell activation could be enhanced by autocrine and paracrine mechanisms depending on the biology of the TLR ligand tested. We determined that depoted ligands can functionally persist on plasma membranes for up to four days in naïve and activated T cells, enhancing their activation, proliferation, and skewing cytokine secretion. Depoted ligands provide a persistent yet non-permanent adjuvant signal to immune cells that may minimize the intensity and duration of toxicities compared to permanent genetic delivery. Altogether, these findings demonstrate potential for lipid-mediated insertion (depoting) as a universal cell engineering approach with unique, complementary advantages to other cell engineering methods.

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Pan-Cancer Analysis of PIMREG as a Biomarker for the Prognostic and Immunological Role

Frontiers in Genetics ◽

10.3389/fgene.2021.687778 ◽

2021 ◽

Vol 12 ◽

Author(s):

Hua Zhu ◽

Xinyao Hu ◽

Yingze Ye ◽

Zhihong Jian ◽

Yi Zhong ◽

...

Keyword(s):

Signaling Pathway ◽

Chemokine Receptors ◽

Antigen Processing ◽

Immune Cell ◽

Nk Cell ◽

Cell Lineage ◽

Cell Receptor ◽

The Cancer Genome Atlas ◽

Cancer Types ◽

Pan Cancer

Phosphatidylinositol binding clathrin assembly protein interacting mitotic regulator (PIMREG) localizes to the nucleus and can significantly elevate the nuclear localization of clathrin assembly lymphomedullary leukocythemia gene. Although there is some evidence to support an important action for PIMREG in the occurrence and development of certain cancers, currently no pan-cancer analysis of PIMREG is available. Therefore, we intended to estimate the prognostic predictive value of PIMREG and to explore its potential immune function in 33 cancer types. By using a series of bioinformatics approaches, we extracted and analyzed datasets from Oncomine, The Cancer Genome Atlas, Cancer Cell Lineage Encyclopedia (CCLE) and the Human Protein Atlas (HPA), to explore the underlying carcinogenesis of PIMREG, including relevance of PIMREG to prognosis, microsatellite instability (MSI), tumor mutation burden (TMB), tumor microenvironment (TME) and infiltration of immune cells in various types of cancer. Our findings indicate that PIMREG is highly expressed in at least 24 types of cancer, and is negatively correlated with prognosis in major cancer types. In addition, PIMREG expression was correlated with TMB in 24 cancers and with MSI in 10 cancers. We revealed that PIMREG is co-expressed with genes encoding major histocompatibility complex, immune activation, immune suppression, chemokine and chemokine receptors. We also found that the different roles of PIMREG in the infiltration of different immune cell types in different tumors. PIMREG can potentially influence the etiology or pathogenesis of cancer by acting on immune-related pathways, chemokine signaling pathway, regulation of autophagy, RIG-I like receptor signaling pathway, antigen processing and presentation, FC epsilon RI pathway, complement and coagulation cascades, T cell receptor pathway, NK cell mediated cytotoxicity and other immune-related pathways. Our study suggests that PIMREG can be applied as a prognostic marker in a variety of malignancies because of its role in tumorigenesis and immune infiltration.

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Immune cell engineering: opportunities in lung cancer therapeutics

Drug Delivery and Translational Research ◽

10.1007/s13346-020-00719-2 ◽

2020 ◽

Vol 10 (5) ◽

pp. 1203-1227

Author(s):

Arpit Bhargava ◽

Dinesh Kumar Mishra ◽

Rajnarayan Tiwari ◽

Nirmal Kumar Lohiya ◽

Irina Yu Goryacheva ◽

...

Keyword(s):

Lung Cancer ◽

Immune Cell ◽

Cancer Therapeutics ◽

Cell Engineering

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A mikro-RNS-ek jelentősége szisztémás autoimmun betegségek kialakulásában

Orvosi Hetilap ◽

10.1556/650.2019.31349 ◽

2019 ◽

Vol 160 (15) ◽

pp. 563-572 ◽

Cited By ~ 1

Author(s):

Ilona Jámbor ◽

Krisztina Szabó ◽

Margit Zeher ◽

Gábor Papp

Keyword(s):

Autoimmune Diseases ◽

Lupus Erythematosus ◽

Immune Cell ◽

Cell Lineage ◽

Therapeutic Approaches ◽

Systemic Autoimmune Diseases ◽

Protein Coding ◽

Diagnosis And Prognosis ◽

Research Findings ◽

Posttranscriptional Level

Abstract: MicroRNAs (miRNAs) are 18–25 nucleotide long, single stranded, endogenous, non-coding small RNAs playing an important role in regulating gene expression at posttranscriptional level. miRNAs control approximately 90% of protein-coding genes, and play a central role in various biological processes including immune cell lineage commitment, differentiation, proliferation, apoptosis and maintenance of immune homeostasis. Changes in the expression of certain miRNAs may lead to the development of many diseases, including systemic autoimmune diseases. In this study, we summarize the biogenesis of miRNAs, their role in regulation of the immune system, and review the latest research findings in systemic lupus erythematosus, primary Sjögren’s syndrome, rheumatoid arthritis and systemic sclerosis. In the future, miRNAs may help not only in establishing diagnosis and prognosis but potentially serve as targets for modern therapeutic approaches in autoimmune diseases. Orv Hetil. 2019; 160(15): 563–572.

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Identification of Potential Diagnostic Gene Targets for Pediatric Sepsis Based on Bioinformatics and Machine Learning

Frontiers in Pediatrics ◽

10.3389/fped.2021.576585 ◽

2021 ◽

Vol 9 ◽

Author(s):

Ying Qiao ◽

Bo Zhang ◽

Ying Liu

Keyword(s):

Prediction Model ◽

Differentially Expressed Genes ◽

Immune Cell ◽

Cell Lineage ◽

Enrichment Analysis ◽

Differentially Expressed ◽

Significant Difference ◽

Neutrophil Degranulation ◽

Hematopoietic Cell Lineage ◽

Pediatric Sepsis

Purpose: To develop a comprehensive differential expression gene profile as well as a prediction model based on the expression analysis of pediatric sepsis specimens.Methods: In this study, compared with control specimens, a total of 708 differentially expressed genes in pediatric sepsis (case–control at a ratio of 1:3) were identified, including 507 up-regulated and 201 down-regulated ones. The Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis of differentially expressed genes indicated the close interaction between neutrophil activation, neutrophil degranulation, hematopoietic cell lineage, Staphylococcus aureus infection, and periodontitis. Meanwhile, the results also suggested a significant difference for 16 kinds of immune cell compositions between two sample sets. The two potential selected biomarkers (MMP and MPO) had been validated in septic children patients by the ELISA method.Conclusion: This study identified two potential hub gene biomarkers and established a differentially expressed genes-based prediction model for pediatric sepsis, which provided a valuable reference for future clinical research.

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Comprehensive mapping of the human cytokine gene regulatory network

10.1101/2020.05.05.079657 ◽

2020 ◽

Author(s):

CS Santoso ◽

Z Li ◽

S Lal ◽

S Yuan ◽

KA Gan ◽

...

Keyword(s):

Gene Expression ◽

Transcriptional Control ◽

Immune Cell ◽

Cell Lineage ◽

Cytokine Gene Expression ◽

Gene Promoters ◽

Cytokine Gene ◽

Cytokine Regulation ◽

Gene Regulatory ◽

Human Cytokine

SummaryProper cytokine gene expression is essential in development, homeostasis, and immune responses. Studies on the transcriptional control of cytokine genes have mostly focused on highly researched transcription factors (TFs) and cytokines, resulting in an incomplete portrait of cytokine gene regulation. Here, we use enhanced yeast one-hybrid (eY1H) assays to derive a comprehensive network comprising 1,380 interactions between 265 TFs and 108 cytokine gene promoters, greatly expanding the known repertoire of TF-cytokine gene interactions. We found an enrichment of nuclear receptors and confirmed their role in cytokine regulation in primary macrophages. Additionally, we used the eY1H-derived network as a framework to identify pairs of TFs that synergistically modulate cytokine gene expression, and to identify novel TF-cytokine regulatory axes in immune diseases and immune cell lineage development. Overall, the eY1H data provides a rich resource to study cytokine regulation in a variety of physiological and disease contexts.

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Single-cell transcriptomics reveal the heterogeneity and dynamic of cancer stem-like cells during breast tumor progression

Cell Death and Disease ◽

10.1038/s41419-021-04261-y ◽

2021 ◽

Vol 12 (11) ◽

Author(s):

Guojuan Jiang ◽

Juchuanli Tu ◽

Lei Zhou ◽

Mengxue Dong ◽

Jue Fan ◽

...

Keyword(s):

Breast Cancer ◽

Epithelial Cell ◽

Epithelial Cells ◽

Tumor Progression ◽

Single Cell ◽

Immune Cells ◽

Breast Tumor ◽

Immune Cell ◽

Cell Lineage ◽

Breast Tumor Progression

AbstractBreast cancer stem-like cells (BCSCs) play vital roles in tumorigenesis and progression. However, the origin and dynamic changes of BCSCs are still to be elucidated. Using the breast cancer mouse model MMTV-PyMT, we constructed a single-cell atlas of 31,778 cells from four distinct stages of tumor progression (hyperplasia, adenoma/MIN, early carcinoma and late carcinoma), during which malignant transition occurs. We identified that the precise cell type of ERlow epithelial cell lineage gave rise to the tumors, and the differentiation of ERhigh epithelial cell lineage was blocked. Furthermore, we discovered a specific signature with a continuum of gene expression profiles along the tumor progression and significantly correlated with clinical outcomes, and we also found a stem-like cell cluster existed among ERlow epithelial cells. Further clustering on this stem-like cluster showed several sub-clusters indicating heterogeneity of stem-like epithelial cells. Moreover, we distinguished normal and cancer stem-like cells in this stem-like epithelial cell cluster and profiled the molecular portraits from normal stem-like cell to cancer stem-like cells during the malignant transition. Finally, we found the diverse immune cell infiltration displayed immunosuppressive characteristics along tumor progression. We also found the specific expression pattern of cytokines and their corresponding cytokine receptors in BCSCs and immune cells, suggesting the possible cross-talk between BCSCs and the immune cells. These data provide a useful resource for illuminating BCSC heterogeneity and the immune cell remodeling during breast tumor progression, and shed new light on transcriptomic dynamics during the progression at the single-cell level.

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MicroRNA-155 Regulates MAIT1 and MAIT17 Cell Differentiation

Frontiers in Cell and Developmental Biology ◽

10.3389/fcell.2021.670531 ◽

2021 ◽

Vol 9 ◽

Author(s):

Tingting Liu ◽

Jie Wang ◽

Kalpana Subedi ◽

Qijun Yi ◽

Li Zhou ◽

...

Keyword(s):

Immune Cell ◽

Cell Lineage ◽

Cell Development ◽

Loss Of Function ◽

Mait Cells ◽

Cellular Processes ◽

Individual Mirnas ◽

Maturation Stages ◽

And Function ◽

Mait Cell

Mucosal-associated invariant T (MAIT) cells are innate-like T cells that develop in the thymus through three maturation stages to acquire effector function and differentiate into MAIT1 (T-bet+) and MAIT17 (RORγt+) subsets. Upon activation, MAIT cells release IFN-γ and IL-17, which modulate a broad spectrum of diseases. Recent studies indicate defective MAIT cell development in microRNA deficient mice, however, few individual miRNAs have been identified to regulate MAIT cells. MicroRNA-155 (miR-155) is a key regulator of numerous cellular processes that affect some immune cell development, but its role in MAIT cell development remains unclear. To address whether miR-155 is required for MAIT cell development, we performed gain-of-function and loss-of-function studies. We first generated a CD4Cre.miR-155 knock-in mouse model, in which miR-155 is over-expressed in the T cell lineage. We found that overexpression of miR-155 significantly reduced numbers and frequencies of MAIT cells in all immune organs and lungs and blocked thymic MAIT cell maturation through downregulating PLZF expression. Strikingly, upregulated miR-155 promoted MAIT1 differentiation and blocked MAIT17 differentiation, and timely inducible expression of miR-155 functionally inhibited peripheral MAIT cells secreting IL-17. miR-155 overexpression also increased CD4–CD8+ subset and decreased CD4–CD8– subset of MAIT cells. We further analyzed MAIT cells in conventional miR-155 knockout mice and found that lack of miR-155 also promoted MAIT1 differentiation and blocked MAIT17 differentiation but without alteration of their overall frequency, maturation and function. Overall, our results indicate that adequate miR-155 expression is required for normal MAIT1 and MAIT17 cell development and function.

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IMMU-38. DEEP IMMUNOPROFILING OF HUMAN GLIOBLASTOMA (GBM) REVEALS DIFFERENCES IN THE TUMOR IMMUNE CELL INFILTRATE IN PATIENTS WITH HIGH VS. LOW PLASMA CELL-FREE DNA (CFDNA)

Neuro-Oncology ◽

10.1093/neuonc/noab196.397 ◽

2021 ◽

Vol 23 (Supplement_6) ◽

pp. vi100-vi101

Author(s):

Stephen J Bagley ◽

Cecile Alanio ◽

Jacob Till ◽

Aseel Abdalla ◽

Zev Binder ◽

...

Keyword(s):

T Cells ◽

Immune Cell ◽

Cell Lineage ◽

Predictive Biomarker ◽

High Plasma ◽

Lineage Differentiation ◽

Tumor Infiltrate ◽

Poor Outcomes ◽

And Function ◽

Immune Cell Infiltrates

Abstract BACKGROUND We have previously demonstrated that high baseline plasma cfDNA concentration is associated with poor survival in patients with newly diagnosed GBM. The mechanism of this association remains unknown. To explore whether differences in the immune landscape between high- vs. low-cfDNA patients may play a role in their divergent clinical outcomes, we phenotyped tumors from patients with high vs. low cfDNA using mass cytometry by time of flight (CyTOF). METHODS We performed CyTOF on frozen tumor infiltrate suspension from a pilot cohort of patients with previously untreated GBM with known baseline plasma cfDNA concentration (Bagley, Clin Cancer Res 2020). CyTOF was used to simultaneously measure expression of 39 molecules related to immune cell lineage, differentiation state, and function. Differences in immune cell infiltrates between high- and low-cfDNA patients were assessed using Mann-Whitney U tests. RESULTS Four patients with high cfDNA (median 57, range 33-90 ng/mL) were compared to six patients with low cfDNA (median 12, range 7-16 ng/mL). Immune cell infiltrates with increased adaptive cells (high monocytes and T cells, p=0.05) were present in high-cfDNA compared to low-cfDNA patients. While > 70% of the infiltrating T cells were exhausted in both groups, the pattern of exhaustion was significantly different in high- vs. low-cfDNA patients, with less CXCR5+CD69+ and more CXCR5-CD69- (p=0.008) progenitor exhausted T cells in cfDNA-high patients. CONCLUSIONS In this GBM pilot study, we demonstrated differences in the tumor immune infiltrate in patients with high vs. low baseline plasma cfDNA concentration. Preclinical studies will be needed to determine if this explains the association between high plasma cfDNA and poor outcomes previously observed in patients. Our results may have implications for the use of cfDNA concentration as a predictive biomarker for immunotherapy, as tumors with more intermediate progenitor (CXCR5-CD69-) exhausted T cells may respond better to PD-1 checkpoint blockade.

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Lineage Decision-Making within Normal Haematopoietic and Leukemic Stem Cells

International Journal of Molecular Sciences ◽

10.3390/ijms21062247 ◽

2020 ◽

Vol 21 (6) ◽

pp. 2247

Author(s):

Geoffrey Brown ◽

Lucía Sánchez ◽

Isidro Sánchez-García

Keyword(s):

Stem Cells ◽

Cell Fate ◽

Immune Cell ◽

Alternative Pathway ◽

Cell Lineage ◽

Cell Types ◽

Haematopoietic Stem Cell ◽

Haematopoietic Stem Cells ◽

Wide Range ◽

Lineage Decision

To produce the wide range of blood and immune cell types, haematopoietic stem cells can “choose” directly from the entire spectrum of blood cell fate-options. Affiliation to a single cell lineage can occur at the level of the haematopoietic stem cell and these cells are therefore a mixture of some pluripotent cells and many cells with lineage signatures. Even so, haematopoietic stem cells and their progeny that have chosen a particular fate can still “change their mind” and adopt a different developmental pathway. Many of the leukaemias arise in haematopoietic stem cells with the bulk of the often partially differentiated leukaemia cells belonging to just one cell type. We argue that the reason for this is that an oncogenic insult to the genome “hard wires” leukaemia stem cells, either through development or at some stage, to one cell lineage. Unlike normal haematopoietic stem cells, oncogene-transformed leukaemia stem cells and their progeny are unable to adopt an alternative pathway.

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