Intercellular communication and cell-cell adhesion

Single-cell omics: experimental workflow, data analyses and applications

Cells are the fundamental units of biological systems and exhibit unique development trajectories and molecular features. Our exploration of how the genomes orchestrate the formation and maintenance of each cell, and control the cellular phenotypes of various organismsis, is both captivating and intricate. Since the inception of the first single-cell RNA technology, technologies related to single-cell sequencing have experienced rapid advancements in recent years. These technologies have expanded horizontally to include single-cell genome, epigenome, proteome, and metabolome, while vertically, they have progressed to integrate multiple omics data and incorporate additional information such as spatial scRNA-seq and CRISPR screening. Single-cell omics represent a groundbreaking advancement in the biomedical field, offering profound insights into the understanding of complex diseases, including cancers. Here, we comprehensively summarize recent advances in single-cell omics technologies, with a specific focus on the methodology section. This overview aims to guide researchers in selecting appropriate methods for single-cell sequencing and related data analysis.

Targeting cancer-derived extracellular vesicles by combining CD147 inhibition with tissue factor pathway inhibitor for the management of urothelial cancer cells

BACKGROUND

Extracellular vesicles (EVs), including microvesicles, hold promise for the management of bladder urothelial carcinoma (BLCA), particularly because of their utility in identifying therapeutic targets and their diagnostic potential using easily accessible urine samples. Among the transmembrane glycoproteins highly enriched in cancer-derived EVs, tissue factor (TF) and CD147 have been implicated in promoting tumor progression. In this in vitro study, we explored a novel approach to impede cancer cell migration and metastasis by simultaneously targeting these molecules on urothelial cancer-derived EVs.

METHODS

Cell culture supernatants from invasive and non-invasive bladder cancer cell lines and urine samples from patients with BLCA were collected. Large, microvesicle-like EVs were isolated using sequential centrifugation and characterized by electron microscopy, nanoparticle tracking analysis, and flow cytometry. The impact of urinary or cell supernatant-derived EVs on cellular phenotypes was evaluated using cell-based assays following combined treatment with a specific CD147 inhibitor alone or in combination with a tissue factor pathway inhibitor (TFPI), an endogenous anticoagulant protein that can be released by low-molecular-weight heparins.

RESULTS

We observed that EVs obtained from the urine samples of patients with muscle-invasive BLCA and from the aggressive bladder cancer cell line J82 exhibited higher TF activity and CD147 expression levels than did their non-invasive counterparts. The shedding of GFP-tagged CD147 into isolated vesicles demonstrated that the vesicles originated from plasma cell membranes. EVs originating from invasive cancer cells were found to trigger migration, secretion of matrix metalloproteinases (MMPs), and invasion. The same induction of MMP activity was replicated using EVs obtained from urine samples of patients with invasive BLCA. EVs derived from cancer cell clones overexpressing TF and CD147 were produced in higher quantities and exhibited a higher invasive potential than those from control cancer cells. TFPI interfered with the effect when used in conjunction with the CD147 inhibitor, further suppressing homotypic EV-induced migration, MMP production, and invasion.

CONCLUSIONS

Our findings suggest that combining a CD147 inhibitor with low molecular weight heparins to induce TFPI release may be a promising therapeutic approach for urothelial cancer management. This combination can potentially suppress the tumor-promoting actions of cancer-derived microvesicle-like EVs, including collective matrix invasion.

Defining and identifying cell sub-crosstalk pairs for characterizing cell-cell communication patterns

Current cell-cell communication analysis focuses on quantifying intercellular interactions at cell type level. In the tissue microenvironment, one type of cells could be divided into multiple cell subgroups that function differently and communicate with other cell types or subgroups via different ligand-receptor-mediated signaling pathways. Given two cell types, we define a cell sub-crosstalk pair (CSCP) as a combination of two cell subgroups with strong and similar intercellular crosstalk signals and identify CSCPs based on coupled non-negative matrix factorization. Using single-cell spatial transcriptomics data of mouse olfactory bulb and visual cortex, we find that cells of different types within CSCPs are significantly spatially closer with each other than those in the whole single-cell spatial map. To demonstrate the utility of CSCPs, we apply 13 cell-cell communication analysis methods to sampled single-cell transcriptomics datasets at CSCP level and reveal ligand-receptor interactions masked at cell type level. Furthermore, by analyzing single-cell transcriptomics data from 29 breast cancer patients with different immunotherapy responses, we find that CSCPs are useful predictive features to discriminate patients responding to anti-PD-1 therapy from non-responders. Taken together, partitioning a cell type pair into CSCPs enables fine-grained characterization of cell-cell communication in tissue and tumor microenvironments.

RobustCCC: a robustness evaluation tool for cell-cell communication methods

Cell-cell communication (CCC) inference has become a routine task in single-cell data analysis. Many computational tools are developed for this purpose. However, the robustness of existing CCC methods remains underexplored. We develop a user-friendly tool, RobustCCC, to facilitate the robustness evaluation of CCC methods with respect to three perspectives, including replicated data, transcriptomic data noise and prior knowledge noise. RobustCCC currently integrates 14 state-of-the-art CCC methods and 6 simulated single-cell transcriptomics datasets to generate robustness evaluation reports in tabular form for easy interpretation. We find that these methods exhibit substantially different robustness performances using different simulation datasets, implying a strong impact of the input data on resulting CCC patterns. In summary, RobustCCC represents a scalable tool that can easily integrate more CCC methods, more single-cell datasets from different species (e.g., mouse and human) to provide guidance in selecting methods for identification of consistent and stable CCC patterns in tissue microenvironments. RobustCCC is freely available at https://github.com/GaoLabXDU/RobustCCC.

Landscape of Exhausted T Cells in Tuberculosis Revealed by Single-Cell Sequencing

Tuberculosis, a contagious bacterial infection caused by Mycobacterium tuberculosis, is a substantial global health problem, impacting millions of lives annually. Exhausted T-cell signatures are critical for predicting clinical responses to tuberculosis infection. To obtain a panoramic transcriptional profile of T cells, we performed single-cell RNA-sequencing analysis of CD4+ T and CD8+ T cells isolated from peripheral blood mononuclear cells of healthy individuals and patients with tuberculosis. We identified seven subsets in CD8+ T cells and eight subsets in CD4+ T cells and elucidated the transcriptomic landscape changes and characteristics of each subset. We further investigated the cell-to-cell relationship of each subgroup of the two cell types. Different signature genes and pathways of exhausted CD4+ and CD8+ T cells were examined. We identified 12 genes with potential associations of T-cell exhaustion after tuberculosis infection. We also identified five genes as potential exhaustion marker genes. The CD8-EX3 subcluster in CD8+ T-exhausted cells was identified as an exhaustion-specific subcluster. The identified gene module further clarified the key factors influencing CD8+ T cell exhaustion. These data provide new insights into T-cell signatures in tuberculosis-exhausted populations. IMPORTANCE Identifying the changes in immune cells in response to infection can provide a better understanding of the effects of Mycobacterium tuberculosis on the host immune system. We performed single-cell RNA-sequencing analysis of CD4+ T and CD8+ T cells isolated from peripheral blood mononuclear cells of healthy individuals and patients with tuberculosis to reveal the cellular characteristics. Different signature genes and pathways of exhausted CD4+ and CD8+ T cells were examined. These will facilitate a more comprehensive understanding of the onset and underlying mechanism of T-cell exhaustion during active Mtb infection.

Platelets play a dual role in the pathophysiology of transfusion-related acute lung injury

Platelets are increasingly recognized as key regulators of inflammatory and immune responses, through their interaction with endothelium and immune cells. Therefore they might have a role in transfusion-related acute lung injury (TRALI), in which endothelial cells and neutrophils are the key players. In this study, by a classic TRALI animal model, combining a custom-designed system for intravital confocal microscopy of pulmonary microvasculature and a platelet tracking technique, we found that thrombin-activated platelets transfusion aggravated TRALI while resting platelets transfusion alleviated TRALI. Promoting endogenous platelets activation also aggravated TRALI while inhibiting endogenous platelets activation alleviated TRALI. Activated platelets interfered with the stability of endothelial barrier function while resting platelets modulated the activation of neutrophils. Anti-thrombin could alleviate TRALI, which was not reproduced upon anti-GPIIbIIIa or anti-P-selectin In conclusion, platelets might play a dual role (protective and pathogenic) in TRALI, the balance between the two roles is highly dependent on whether platelets are activated by thrombin or not. This might explain the conflicting results of previous researches studying the contribution of platelets in TRALI by platelet depletion technology, in which the induction of TRALI and the condition of animals were different, hence the state of platelets during TRALI was different. Moreover, anti-platelet-activation (such as anti-thrombin) might be a better approach than anti-activated-platelets (such as anti-P-selectin) to search for potential therapies in TRALI. Considering the involvement of thrombin-activated platelets in TRALI, anti-thrombin might be needed when blood component transfusion is performed.

Melanoma molecular subtyping and scoring model construction based on ligand-receptor pairs

Melanoma is a malignancy of melanocytes, responsible for a high percentage of skin cancer mortality. Ligand-Receptor pairs, a type of cellular communication, are essential for tumor genesis, growth, metastasis, and prognosis. Yet, the role of Ligand-Receptor pairs in melanoma has not been fully elucidated. Our research focused on the function of Ligand-Receptor pairs in melanoma prognosis. We screened 131 melanoma prognosis corresponded ligand-receptor pairs by analyzing the TCGA data of melanoma and the 2293 LR pairs retrieved from the connectomeDB2020 database. And further developed subtypes of melanoma according to the expression of these ligand-receptor pairs by Consensus Clustering. Then we using lasso cox regression and stepwise multivariate regression analysis established a ligand-receptor pairs-based scoring model for the evaluation of melanoma prognosis. Our study demonstrated that the ligand-receptor pairs are vital to the molecular heterogeneity of melanoma, and characterized three different melanoma ligand-receptor pairs subtypes. Among them, the C3 subtype showed a better prognosis, while the C1 subtype exhibited a low prognosis state. And our analysis then found out that this could be related to the differed activation and inhabitation of the cell cycle and immune-related pathways. Using lasso cox regression and stepwise multivariate regression analysis, we further identified 9 key ligand-receptor pairs and established a scoring model that effectively correlated with the prognosis, immune pathways, and therapy of melanoma, showing that the LR.score model was a trustworthy and independent biomarker for melanoma prognosis evaluation. In sum, we found that ligand-receptor pairs are significantly associated with the prognosis and therapy of melanoma. And our ligand-receptor-based scoring model showed potential for the evaluation of melanoma prognosis and immune therapy outcome prediction, which is crucial to the survival for the patients.

Mutant MESD links cellular stress to type I collagen aggregation in osteogenesis imperfecta type XX

Aberrant forms of endoplasmic reticulum (ER)-resident chaperones are implicated in loss of protein quality control in rare diseases. Here we report a novel mutation (p.Asp233Asn) in the ER retention signal of MESD by whole exome sequencing of an individual diagnosed with osteogenesis imperfecta (OI) type XX. While MESDD233N has similar stability and chaperone activity as wild-type MESD, its mislocalization to cytoplasm leads to imbalance of ER proteostasis, resulting in improper folding and aggregation of proteins, including LRP5 and type I collagen. Aggregated LRP5 loses its plasma membrane localization to disrupt the expression of WNT-responsive genes, such as BMP2, BMP4, in proband fibroblasts. We show that MESD is a direct chaperone of pro-α1(I) [COL1A1], and absence of MESDD233N in ER results in cytosolic type I collagen aggregates that remain mostly not secreted. While cytosolic type I collagen aggregates block the intercellular nanotubes, decreased extracellular type I collagen also results in loss of interaction of ITGB1 with type I collagen and weaker attachment of fibroblasts to matrix. Although proband fibroblasts show increased autophagy to degrade the aggregated type I collagen, an overall cellular stress overwhelms the proband fibroblasts. In summary, we present an essential chaperone function of MESD for LRP5 and type I collagen and demonstrating how the D233N mutation in MESD correlates with impaired WNT signaling and proteostasis in OI.

T cell-derived exosomes in tumor immune modulation and immunotherapy

Exosomes are nanoscale vesicles secreted by most cells and have a phospholipid bilayer structure. Exosomes contain DNA, small RNA, proteins, and other substances that can carry proteins and nucleic acids and participate in communication between cells. T cells are an indispensable part of adaptive immunity, and the functions of T cell-derived exosomes have been widely studied. In the more than three decades since the discovery of exosomes, several studies have revealed that T cell-derived exosomes play a novel role in cell-to-cell signaling, especially in the tumor immune response. In this review, we discuss the function of exosomes derived from different T cell subsets, explore applications in tumor immunotherapy, and consider the associated challenges.

CITEdb: a manually curated database of cell-cell interactions in human

MOTIVATION

The interactions among various types of cells play critical roles in cell functions and the maintenance of the entire organism. While cell-cell interactions are traditionally revealed from experimental studies, recent developments in single-cell technologies combined with data mining methods have enabled computational prediction of cell-cell interactions, which have broadened our understanding of how cells work together, and have important implications in therapeutic interventions targeting cell-cell interactions for cancers and other diseases. Despite the importance, to our knowledge, there is no database for systematic documentation of high-quality cell-cell interactions at the cell type level, which hinders the development of computational approaches to identify cell-cell interactions.

RESULTS

We develop a publicly accessible database, CITEdb (Cell-cell InTEraction database, https://citedb.cn/), which not only facilitates interactive exploration of cell-cell interactions in specific physiological contexts (e.g. a disease or an organ) but also provides a benchmark dataset to interpret and evaluate computationally derived cell-cell interactions from different tools. CITEdb contains 728 pairs of cell-cell interactions in human that are manually curated. Each interaction is equipped with structured annotations including the physiological context, the ligand-receptor pairs that mediate the interaction, etc. Our database provides a web interface to search, visualize and download cell-cell interactions. Users can search for cell-cell interactions by selecting the physiological context of interest or specific cell types involved. CITEdb is the first attempt to catalogue cell-cell interactions at the cell type level, which is beneficial to both experimental, computational and clinical studies of cell-cell interactions.

AVAILABILITY AND IMPLEMENTATION

CITEdb is freely available at https://citedb.cn/ and the R package implementing benchmark is available at https://github.com/shanny01/benchmark.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Connexin-Based Channels in the Liver

Connexin proteins oligomerize in hexameric structures called connexin hemichannels, which then dock to form gap junctions. Gap junctions direct cell-cell communication by allowing the exchange of small molecules and ions between neighboring cells. In this way, hepatic gap junctions support liver homeostasis. Besides serving as building blocks for gap junctions, connexin hemichannels provide a pathway between the intracellular and the extracellular environment. The activation of connexin hemichannels is associated with acute and chronic liver pathologies. This article discusses the role of gap junctions and connexin hemichannels in the liver. © 2022 American Physiological Society. Compr Physiol 12:1-17, 2022.

Cell-Cell Interactions Drive Metastasis of Circulating Tumor Microemboli

Circulating tumor cells are the cellular mediators of distant metastasis in solid malignancies. Their metastatic potential can be augmented by clustering with other tumor cells or nonmalignant cells, forming circulating tumor microemboli (CTM). Cell-cell interactions are key regulators within CTM that convey enhanced metastatic properties, including improved cell survival, immune evasion, and effective extravasation into distant organs. However, the cellular and molecular mechanism of CTM formation, as well as the biology of interactions between tumor cells and immune cells, platelets, and stromal cells in the circulation, remains to be determined. Here, we review the current literature on cell-cell interactions in homotypic and heterotypic CTM and provide perspectives on therapeutic strategies to attenuate CTM-mediated metastasis by targeting cell-cell interactions.

Logic-Gated Proximity Aptasensing for Cell-Surface Real-Time Monitoring of Apoptosis

In nature, intact apoptotic cells release ATP as a signaling molecule to trigger prompt phagocytic clearance, even at the earliest stage of apoptosis. Inspired by this, here we introduce a straightforward strategy for real-time monitoring ATP exocytosis and drug-stimulated apoptosis in the cancer cell surroundings. Triplex-boosted G-quadruplexes (tb-G4s) responding to cell environmental factors (H⁺ and K⁺ ) are engineered to construct a DNA logic-gated nanoplatform for proximity ATP aptasensing on the cell surface. It enables the real-time monitoring of cell apoptosis by capturing released endogenous ATP during chemotherapy drug stimulation, providing a sensitive approach for dynamically evaluating drug-induced apoptosis and therapeutic efficacy.

Applications and analytical tools of cell communication based on ligand-receptor interactions at single cell level

BACKGROUND

Cellular communication is an essential feature of multicellular organisms. Binding of ligands to their homologous receptors, which activate specific cell signaling pathways, is a basic type of cellular communication and intimately linked to many degeneration processes leading to diseases.

MAIN BODY

This study reviewed the history of ligand-receptor and presents the databases which store ligand-receptor pairs. The recently applications and research tools of ligand-receptor interactions for cell communication at single cell level by using single cell RNA sequencing have been sorted out.

CONCLUSION

The summary of the advantages and disadvantages of analysis tools will greatly help researchers analyze cell communication at the single cell level. Learning cell communication based on ligand-receptor interactions by single cell RNA sequencing gives way to developing new target drugs and personalizing treatment.

Redox switching of an artificial transmembrane signal transduction system

Transmission of chemical signals across lipid bilayer membranes can be achieved using membrane-anchored molecules, where molecular motion across the bilayer is controlled by switching the polarity of two different head groups. An external redox signal delivered by ascorbic acid was used to trigger membrane translocation in a synthetic transduction system.

Machine Intelligence in Single-Cell Data Analysis: Advances and New Challenges

The rapid development of single-cell technologies allows for dissecting cellular heterogeneity at different omics layers with an unprecedented resolution. In-dep analysis of cellular heterogeneity will boost our understanding of complex biological systems or processes, including cancer, immune system and chronic diseases, thereby providing valuable insights for clinical and translational research. In this review, we will focus on the application of machine learning methods in single-cell multi-omics data analysis. We will start with the pre-processing of single-cell RNA sequencing (scRNA-seq) data, including data imputation, cross-platform batch effect removal, and cell cycle and cell-type identification. Next, we will introduce advanced data analysis tools and methods used for copy number variance estimate, single-cell pseudo-time trajectory analysis, phylogenetic tree inference, cell-cell interaction, regulatory network inference, and integrated analysis of scRNA-seq and spatial transcriptome data. Finally, we will present the latest analyzing challenges, such as multi-omics integration and integrated analysis of scRNA-seq data.

Bioinspired Protein-Based Assembling: Toward Advanced Life-Like Behaviors

The ability of living organisms to perform structure, energy, and information-related processes for molecular self-assembly through compartmentalization and chemical transformation can possibly be mimicked via artificial cell models. Recent progress in the development of various types of functional microcompartmentalized ensembles that can imitate rudimentary aspects of living cells has refocused attention on the important question of how inanimate systems can transition into living matter. Hence, herein, the most recent advances in the construction of protein-bounded microcompartments (proteinosomes), which have been exploited as a versatile synthetic chassis for integrating a wide range of functional components and biochemical machineries, are critically summarized. The techniques developed for fabricating various types of proteinosomes are discussed, focusing on the significance of how chemical information, substance transportation, enzymatic-reaction-based metabolism, and self-organization can be integrated and recursively exploited in constructed ensembles. Therefore, proteinosomes capable of exhibiting gene-directed protein synthesis, modulated membrane permeability, spatially confined membrane-gated catalytic reaction, internalized cytoskeletal-like matrix assembly, on-demand compartmentalization, and predatory-like chemical communication in artificial cell communities are specially highlighted. These developments are expected to bridge the gap between materials science and life science, and offer a theoretical foundation for developing life-inspired assembled materials toward various applications.

New avenues for systematically inferring cell-cell communication: through single-cell transcriptomics data

For multicellular organisms, cell-cell communication is essential to numerous biological processes. Drawing upon the latest development of single-cell RNA-sequencing (scRNA-seq), high-resolution transcriptomic data have deepened our understanding of cellular phenotype heterogeneity and composition of complex tissues, which enables systematic cell-cell communication studies at a single-cell level. We first summarize a common workflow of cell-cell communication study using scRNA-seq data, which often includes data preparation, construction of communication networks, and result validation. Two common strategies taken to uncover cell-cell communications are reviewed, e.g., physically vicinal structure-based and ligand-receptor interaction-based one. To conclude, challenges and current applications of cell-cell communication studies at a single-cell resolution are discussed in details and future perspectives are proposed.

The β-Carboline Harmine Induces Actin Dynamic Remodeling and Abrogates the Malignant Phenotype in Tumorigenic Cells

Numerous studies have shown that alteration of actin remodeling plays a pivotal role in the regulation of morphologic and phenotypic changes leading to malignancy. In the present study, we searched for drugs that can regulate actin polymerization and reverse the malignant phenotype in cancer cells. We developed a cell-free high-throughput screening assay for the identification of compounds that induce the actin polymerization in vitro, by fluorescence anisotropy. Then, the potential of the hit compound to restore the actin cytoskeleton and reverse the malignant phenotype was checked in EWS-Fli1-transformed fibroblasts and in B16-F10 melanoma cells. A β-carboline extracted from Peganum harmala (i.e., harmine) is identified as a stimulator of actin polymerization through a mechanism independent of actin binding and requiring intracellular factors involved in a process that regulates actin kinetics. Treatment of malignant cells with non-cytotoxic concentrations of harmine induces the recovery of a non-malignant cell morphology accompanied by reorganization of the actin cytoskeleton, rescued cell–cell adhesion, inhibition of cell motility and loss of anchorage-independent growth. In conclusion, harmine induces the reversion of the malignant phenotype by a process involving the modulation of actin dynamics and is a potential anti-tumor agent acting principally through a non-cytotoxic process.

Engineered extracellular vesicles and their mimetics for clinical translation

Cells secrete extracellular vesicles (EVs) to external environments to achieve cellular homeostasis and cell-to-cell communication. Their therapeutic potential has been constantly spotlighted since they mirror both cytoplasmic and membranous components of parental cells. Meanwhile, growing evidence suggests that EV engineering could further promote EVs with a maximized capacity. In this review, a range of engineering techniques as well as upscaling approaches to exploit EVs and their mimetics are introduced. By laying out the pros and cons of each technique from different perspectives, we sought to provide an overview potentially helpful for understanding the current state of the art EV engineering and a guideline for choosing a suitable technique for engineering EVs. Furthermore, we envision that the advances in each technique will give rise to the combinatorial engineering of EVs, taking us a step closer to a clinical translation of EV-based therapeutics.

Role of T cell-derived exosomes in immunoregulation

Exosomes are small membrane vesicles of endocytic origin that are secreted by most cells. They are composed of a lipid bilayer containing transmembrane proteins and enclosing cytosolic proteins and RNA, mediating intercellular communication between different cell types in the body, and thus influencing various physiological and pathological functions of both recipient and parent cells. For their nanolevel structures with a stable nature and various biological functions, studies of exosomes have been the subject of increasing interest in the past few years. It is widely known that different T cell subsets play important roles in cellular and humoral immunity, and their exosomes were also reported to exert similar biological functions. While several groups reported the secretion of exosomes by various T cells, the systematic summary involved in these exosomes are deficient. In this review, we will summarize the structure and functions of exosomes derived from T cells in recent reports, discuss emerging therapeutic opportunities, and consider the associated challenges.

Extracellular Vesicles Secreted by Atherogenic Macrophages Transfer MicroRNA to Inhibit Cell Migration

OBJECTIVE

During inflammation, macrophages secrete vesicles carrying RNA, protein, and lipids as a form of extracellular communication. In the vessel wall, extracellular vesicles (EVs) have been shown to be transferred between vascular cells during atherosclerosis; however, the role of macrophage-derived EVs in atherogenesis is not known. Here, we hypothesize that atherogenic macrophages secrete microRNAs (miRNAs) in EVs to mediate cell-cell communication and promote proinflammatory and proatherogenic phenotypes in recipient cells.

APPROACH AND RESULTS

We isolated EVs from mouse and human macrophages treated with an atherogenic stimulus (oxidized low-density lipoprotein) and characterized the EV miRNA expression profile. We confirmed the enrichment of miR-146a, miR-128, miR-185, miR-365, and miR-503 in atherogenic EVs compared with controls and demonstrate that these EVs are taken up and transfer exogenous miRNA to naive recipient macrophages. Bioinformatic pathway analysis suggests that atherogenic EV miRNAs are predicted to target genes involved in cell migration and adhesion pathways, and indeed delivery of EVs to naive macrophages reduced macrophage migration both in vitro and in vivo. Inhibition of miR-146a, the most enriched miRNA in atherogenic EVs, reduced the inhibitory effect of EVs on macrophage migratory capacity. EV-mediated delivery of miR-146a repressed the expression of target genes IGF2BP1 (insulin-like growth factor 2 mRNA-binding protein 1) and HuR (human antigen R or ELAV-like RNA-binding protein 1) in recipient cells, and knockdown of IGF2BP1 and HuR using short interfering RNA greatly reduced macrophage migration, highlighting the importance of these EV-miRNA targets in regulating macrophage motility.

CONCLUSIONS

EV-derived miRNAs from atherogenic macrophages, in particular miR-146a, may accelerate the development of atherosclerosis by decreasing cell migration and promoting macrophage entrapment in the vessel wall.

Can Specific Protein-Lipid Interactions Stabilize an Active State of the Beta 2 Adrenergic Receptor?

G-protein-coupled receptors are eukaryotic membrane proteins with broad biological and pharmacological relevance. Like all membrane-embedded proteins, their location and orientation are influenced by lipids, which can also impact protein function via specific interactions. Extensive simulations totaling 0.25 ms reveal a process in which phospholipids from the membrane's cytosolic leaflet enter the empty G-protein binding site of an activated β2 adrenergic receptor and form salt-bridge interactions that inhibit ionic lock formation and prolong active-state residency. Simulations of the receptor embedded in an anionic membrane show increased lipid binding, providing a molecular mechanism for the experimental observation that anionic lipids can enhance receptor activity. Conservation of the arginine component of the ionic lock among Rhodopsin-like G-protein-coupled receptors suggests that intracellular lipid ingression between receptor helices H6 and H7 may be a general mechanism for active-state stabilization.

Exosomal transfer of miR-30a between cardiomyocytes regulates autophagy after hypoxia

Recent studies have indicated a protective role of physiological autophagy in ischemic heart disease. However, the underlying mechanisms of autophagy regulation after ischemia are poorly understood. Exosomes are nano-sized vesicles released from cells that play critical roles in mediating cell-to-cell communication through the transfer of microRNAs. In this study, we observed that miR-30a was highly enriched in exosomes from the serum of acute myocardial infarction (AMI) patients in vivo and culture medium of cardiomyocytes after hypoxic stimulation in vitro. We also found that hypoxia inducible factor (HIF)-1α regulates miR-30a, which efficiently transferred via exosomes between cardiomyocytes after hypoxia. Inhibition of miR-30a or release of exosomes increased the expression of the core autophagy regulators beclin-1, Atg12, and LC3II/LC3I, which contributed to maintaining the autophagic response in cardiomyocytes after hypoxia. Taken together, the present study showed that exosomes from hypoxic cardiomyocytes regulate autophagy by transferring miR-30a in a paracrine manner, which revealed a new pathway of autophagy regulation that might comprise a promising strategy to treat ischemic heart disease.

KEY MESSAGES

miR-30a is highly enriched in exosomes from the serum of AMI patients. Hypoxia induces miR-30a upregulation and enrichment into exosomes. MiR-30a is efficiently transferred via exosomes between hypoxic cardiomyocytes. Inhibition of exosome release contributes to maintaining of autophagy after hypoxia. Inhibition of miR-30a augments autophagy after hypoxia.

Photochemical depolymerisation of dermatan sulfate and analysis of the generated oligosaccharides

Radical depolymerisation is the method of choice for the depolymerisation of glycosaminoglycans (GAGs), especially when enzymatic depolymerisation cannot be performed due to the lack of suitable enzymes. The established Fenton type free radical depolymerisation generates radicals from a solution of H2O2 in the presence of Cu(2+) or Fe(2+). When applied to dermatan sulfate (DS), the Fenton type depolymerisation of DS (Panagos, Thomson, Bavington, & Uhrin, 2012) produced exclusively oligosaccharides with reducing end GalNAc, which was partially oxidised to acetylgalactosaminic acid. We report here the results of the TiO2 catalysed photochemical depolymerisation of DS. NMR analysis of these DS oligosaccharides revealed the presence of reducing end IdoA, observed for the first time. The reducing end acetylgalactosaminic acid was also detected. The photochemical depolymerisation method thus enables preparation of new types of GAG oligosaccharides suitable for further biochemical and biological investigation.

Endogenous signalling control of cell adhesion by using aptamer functionalized biocompatible hydrogel

Design of biological signal-responsive biomaterials is essential for controlling cell-cell and cell-matrix interactions. Herein, we developed a dynamic hydrogel to control cell adhesion with biological signals in a cellular microenvironment. The basic principle was based on using nucleic acid aptamer to recognize cell signalling and control the display of bioligands on the hydrogel. Not only exogenous signalling but also endogenous signalling secreted by surrounding cells could activate the dynamic scaffold and tune the cell adhesion state. Since diverse aptamers have been developed, our design can be extended to multiple biological inputs. The biochemical signal-responsive system will greatly enhance the understanding of complex biological processes as well as the ability to manipulate cellular behaviors.

Thiacalix[4]arene-functionalized vesicles as phosphorescent indicators for pyridoxine detection in aqueous solution

Luminescent DPPC vesicles, decorated by new amphiphilic tetracarboxylate derivatives ofp-tert-butylthiacalix[4]arene with Tb(iii) were used for the selective detection of pyridoxine hydrochloride.

Transcellular chaperone signaling: an organismal strategy for integrated cell stress responses

The ability of each cell within a metazoan to adapt to and survive environmental and physiological stress requires cellular stress-response mechanisms, such as the heat shock response (HSR). Recent advances reveal that cellular proteostasis and stress responses in metazoans are regulated by multiple layers of intercellular communication. This ensures that an imbalance of proteostasis that occurs within any single tissue 'at risk' is protected by a compensatory activation of a stress response in adjacent tissues that confers a community protective response. While each cell expresses the machinery for heat shock (HS) gene expression, the HSR is regulated cell non-autonomously in multicellular organisms, by neuronal signaling to the somatic tissues, and by transcellular chaperone signaling between somatic tissues and from somatic tissues to neurons. These cell non-autonomous processes ensure that the organismal HSR is orchestrated across multiple tissues and that transmission of stress signals between tissues can also override the neuronal control to reset cell- and tissue-specific proteostasis. Here, we discuss emerging concepts and insights into the complex cell non-autonomous mechanisms that control stress responses in metazoans and highlight the importance of intercellular communication for proteostasis maintenance in multicellular organisms.

Exosomes from drug-resistant breast cancer cells transmit chemoresistance by a horizontal transfer of microRNAs

Adriamycin and docetaxel are two agents commonly used in treatment of breast cancer, but their efficacy is often limited by the emergence of chemoresistance. Recent studies indicate that exosomes act as vehicles for exchange of genetic cargo between heterogeneous populations of tumor cells, engendering a transmitted drug resistance for cancer development and progression. However, the specific contribution of breast cancer-derived exosomes is poorly understood. Here we reinforced other's report that human breast cancer cell line MCF-7/S could acquire increased survival potential from its resistant variants MCF-7/Adr and MCF-7/Doc. Additionally, exosomes of the latter, A/exo and D/exo, significantly modulated the cell cycle distribution and drug-induced apoptosis with respect to S/exo. Exosomes pre-treated with RNase were unable to regulate cell cycle and apoptosis resistance, suggesting an RNA-dependent manner. Microarray and polymerase chain reaction for the miRNA expression profiles of A/exo, D/exo, and S/exo demonstrated that they loaded selective miRNA patterns. Following A/exo and D/exo transfer to recipient MCF-7/S, the same miRNAs were significantly increased in acquired cells. Target gene prediction and pathway analysis showed the involvement of miR-100, miR-222, and miR-30a in pathways implicated in cancer pathogenesis, membrane vesiculation and therapy failure. Furthermore, D/exo co-culture assays and miRNA mimics transfection experiments indicated that miR-222-rich D/exo could alter target gene expression in MCF-7/S. Our results suggest that drug-resistant breast cancer cells may spread resistance capacity to sensitive ones by releasing exosomes and that such effects could be partly attributed to the intercellular transfer of specific miRNAs.

The immunologically active oligosaccharides isolated from wheatgrass modulate monocytes via Toll-like receptor-2 signaling

Wheatgrass is one of the most widely used health foods, but its functional components and mechanisms remain unexplored. Herein, wheatgrass-derived oligosaccharides (WG-PS3) were isolated and found to induce CD69 and Th1 cytokine expression in human peripheral blood mononuclear cells. In particular, WG-PS3 directly activated the purified monocytes by inducing the expression of CD69, CD80, CD86, IL-12, and TNF-α but affected NK and T cells only in the presence of monocytes. After further purification and structural analysis, maltoheptaose was identified from WG-PS3 as an immunomodulator. Maltoheptaose activated monocytes via Toll-like receptor 2 (TLR-2) signaling, as discovered by pretreatment of blocking antibodies against Toll-like receptors (TLRs) and also determined by click chemistry. This study is the first to reveal the immunostimulatory component of wheatgrass with well defined molecular structures and mechanisms.

Profound re-organization of cell surface proteome in equine retinal pigment epithelial cells in response to in vitro culturing

The purpose of this study was to characterize the cell surface proteome of native compared to cultured equine retinal pigment epithelium (RPE) cells. The RPE plays an essential role in visual function and represents the outer blood-retinal barrier. We are investigating immunopathomechanisms of equine recurrent uveitis, an autoimmune inflammatory disease in horses leading to breakdown of the outer blood-retinal barrier and influx of autoreactive T-cells into affected horses’ vitrei. Cell surface proteins of native and cultured RPE cells from eye-healthy horses were captured by biotinylation, analyzed by high resolution mass spectrometry coupled to liquid chromatography (LC MS/MS), and the most interesting candidates were validated by PCR, immunoblotting and immunocytochemistry. A total of 112 proteins were identified, of which 84% were cell surface membrane proteins. Twenty-three of these proteins were concurrently expressed by both cell states, 28 proteins exclusively by native RPE cells. Among the latter were two RPE markers with highly specialized RPE functions: cellular retinaldehyde-binding protein (CRALBP) and retinal pigment epithelium-specific protein 65kDa (RPE65). Furthermore, 61 proteins were only expressed by cultured RPE cells and absent in native cells. As we believe that initiating events, leading to the breakdown of the outer blood-retinal barrier, take place at the cell surface of RPE cells as a particularly exposed barrier structure, this differential characterization of cell surface proteomes of native and cultured equine RPE cells is a prerequisite for future studies.

Free circulating ICAM-1 in serum and cerebrospinal fluid of HIV-1 infected patients correlate with TNF-alpha and blood-brain barrier damage

The mechanism for the initiation of blood-brain barrier damage and intrathecal inflammation in patients infected with the human immunodeficiency virus (HIV) is poorly understood. We have recently reported that tumour necrosis factor-alpha (TNF-alpha) mediates active neural inflammation and blood-brain barrier damage in HIV-1 infection. Stimulation of endothelial cells by TNF-alpha induces the expression of intercellular adhesion molecule-1 (ICAM-1), which is an important early marker of immune activation and response. We report herein for the first time the detection of high levels of free circulating ICAM-1 in serum and cerebrospinal fluid of patients with HIV-1 infection. Free circulating ICAM-1 in these patients correlated with TNF-alpha concentrations and with the degree of blood-brain barrier damage and were detected predominantly in patients with neurologic involvement. These findings have important implications for the understanding and investigation of the intrathecal inflammatory response in HIV-1 infection.

Artificial signal transduction with primary and secondary messengers

The complete, entirely artificial, signal-transduction process was realized with a pair of tailored transmembrane units that were equipped with receptor- and reactive sites at both amphiphilic ends. Thus, docking of the primary messenger, transmission of the signal, and release of the secondary messenger could all be imitated in a single experimental setup. The system imitates the signaling principle of receptor tyrosine kinases and employs bisphosphonate head-groups for oligoamine-recognition and a pair of thiol nucleophiles and pyridine disulfide tail-groups for intravesicle S(N)2 displacement. This system operates in a unidirectional fashion, does not suffer from intervesicle competition, and is highly sensitive towards the lipid composition of the membrane and the nature of the primary messenger.

Heparin: an intervenor in cell communication

It was nearly 100 years since heparin was discovered, but the role of this widely used anticoagulant is still remarkably thought provoking now. During pathological processes such as atherosclerosis, inflammation, cancer and infection, phenomena of cell adhesion are ubiquitous and complicated. Heparin exerts anti-adhesion activity appearing as a common mechanism of its potential polypharmacology in those diseases. Furthermore, heparin can bind a variety of signalling molecules such as growth factors, cell surface proteins of pathogens and most notably, cell adhesion molecules. These signalling molecules are involved in cell communication, acting as ligands, receptors and second messengers. Considering that heparan sulphate glycosaminoglycan is increasingly recognized as a key mediator in many cellular processes, the structural similarity with heparan sulphate suggests that heparin is a multifunctional intervenor in cell communication.

Rab35 and its GAP EPI64C in T cells regulate receptor recycling and immunological synapse formation

Upon antigen recognition, T-cell receptor (TCR/CD3) and other signaling molecules become enriched in a specialized contact site between the T cell and antigen-presenting cell, i.e. the immunological synapse (IS). Enrichment occurs via mechanisms that include polarized secretion from recycling endosomes, but the Rabs and RabGAPs that regulate this are unknown. EPI64C (TBC1D10C) is an uncharacterized candidate RabGAP we identified by mass spectrometry as abundant in human peripheral blood T cells that is preferentially expressed in hematopoietic cells. EPI64C is a Rab35-GAP based both on in vitro Rab35-specific GAP activity and findings in transfection assays. EPI64C and Rab35 dominant negative (DN) constructs each impaired transferrin export from a recycling pathway in Jurkat T-cells and induced large vacuoles marked by transferrin receptor, TCR, and SNAREs implicated in TCR-polarized secretion. Rab35 localized to the plasma membrane and to intracellular vesicles where it substantially colocalized with TfR and with TCR. Rab35 was strongly recruited to the IS. Conjugate formation was impaired by transfection with Rab35-DN or EPI64C and by EPI64C knock down. TCR enrichment at the IS was impaired by Rab35-DN. Thus, EPI64C and Rab35 regulate a recycling pathway in T cells and contribute to IS formation, most likely by participating in TCR transport to the IS.

Expression of expanded polyglutamine targets profilin for degradation and alters actin dynamics

Huntington's disease is caused by polyglutamine expansion in the huntingtin protein. Huntingtin directly interacts with profilin, a major actin monomer sequestering protein and a key integrator of signals leading to actin polymerization. We observed a progressive loss of profilin in the cerebral cortex of Huntington's disease patients, and in cell culture and Drosophila models of polyglutamine disease. This loss of profilin is likely due to increased degradation through the ubiquitin proteasome system. Profilin loss reduces the F/G actin ratio, indicating a shift in actin polymerization. Overexpression of profilin abolishes mutant huntingtin toxicity in cells and partially ameliorates the morphological and functional eye phenotype and extends lifespan in a transgenic polyglutamine Drosophila model. These results indicate a link between huntingtin and profilin and implicate profilin in Huntington's disease pathogenesis.

Green tea induces annexin-I expression in human lung adenocarcinoma A549 cells: involvement of annexin-I in actin remodeling

Green tea polyphenols exhibit multiple antitumor activities in various in vitro and in vivo tumor models, and the mechanisms of action are not clear. Previously, we found that green tea extract (GTE) regulates actin remodeling in different cell culture systems. Actin remodeling plays an important role in cancer cell morphology, cell adhesion, motility, and invasion. Using proteomic approaches, we found GTE-induced expression of annexin-I, a multifunctional actin binding protein, in these cell lines. In this study, we aimed to further define the functional role of GTE-induced annexin-I expression in actin remodeling, cell adhesion, and motility in lung adenocarcinoma A549 cells. We found that GTE stimulates the expression of annexin-I in a dose-dependent fashion. The GTE-induced annexin-I expression appears to be at the transcription level, and the increased annexin-I expression mediates actin polymerization, resulting in enhanced cell adhesion and decreased motility. Annexin-I specific interference resulted in loss of GTE-induced actin polymerization and cell adhesion, but not motility. In fact, annexin-I specific interference itself inhibited motility even without GTE. Together, annexin-I plays an important role in GTE-induced actin remodeling, and it may serve as a potential molecular target associated with the anticancer activities of green tea.

Entirely artificial signal transduction with adrenaline

Multifunctional transmembrane-building blocks with recognition sites for adrenaline on one end and the reaction partners for an SN2 reaction on the opposite end have been embedded in DPPC-liposomes. These doped vesicles can be quantitatively reduced at their disulfide head groups by externally added reducing agents; their composition and chemical processes taking place within can be monitored by NMR spectroscopy and--with limitations--by UV/Vis spectroscopy. Attempted release of thiopyridine as a second messenger into the interior of the liposome on external adrenaline addition could not be proven unambiguously because the detection system does not fulfill the necessary rigorous specificity and sensitivity requirements.